table_name column_index column_name column_title datatype scale precision nullable default_value is_auto_inc fk_table fk_column_name is_required input_type input_length onChange is_data_column is_display_column is_key_field column_text optionlist_query url PR_proteomics_experiment 1 experiment_id Experiment ID int 4 0 N Y N N pkDEFAULT PR_proteomics_experiment 2 experiment_request_id Experiment Request ID int 4 0 Y N PR_proteomics_experiment_request experiment_request_id N N PR_proteomics_experiment 3 contact_id Contact int 4 0 N N contact contact_id Y current_contact_id Y Y N PI for this experiment PR_proteomics_experiment 4 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project to which the experiment belongs "SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id " PR_proteomics_experiment 5 experiment_name Experiment Title varchar 100 0 N N Y text 50 Y Y N Title of this experiment PR_proteomics_experiment 6 experiment_tag Experiment Tag varchar 30 0 N N Y text 30 Y Y Y Short tag (name) of this experiment. Treat this like a directory/folder name. Do not use spaces or non-standard characters. PR_proteomics_experiment 7 experiment_description Experiment Description text 16 0 N N Y textarea 6 Y Y N "Description of this experiment, the sample or samples used, and any other relevant information not contained in the project description or in list-box elements in this form" PR_proteomics_experiment 8 experiment_path Experiment Path varchar 255 0 N N Y text 50 Y Y N Data path for this experiment (e.g. /data/search/edeutsch/TCells/T_000/human_nci) PR_proteomics_experiment 9 organism_id Organism int 4 0 N N Y optionlist Y Y N Organism from which the sample used for this experiment was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" PR_proteomics_experiment 10 experiment_type_id Experiment Type int 4 0 N N PR_experiment_type experiment_type_id Y optionlist Y Y N "Type/class of experiment (e.g. d0/d8 ICAT, etc.)" "SELECT experiment_type_id, experiment_type_name FROM $TBPR_EXPERIMENT_TYPE ORDER BY sort_order,experiment_type_name" PR_proteomics_experiment 11 instrument_id Instrument int 4 0 N N PR_instrument instrument_id Y optionlist Y Y N Instrument on which this experiment was performed "SELECT instrument_id, instrument_name FROM $TBPR_INSTRUMENT ORDER BY sort_order,instrument_name" PR_proteomics_experiment 12 gradient_program_id Gradient Program int 4 0 Y N PR_gradient_program gradient_program_id N optionlist Y Y N Gradient Program used for this experiment. Choose MULTIPLE if different programs were used for different msruns within this experiment. "SELECT gradient_program_id,gradient_program_name FROM $TBPR_GRADIENT_PROGRAM WHERE record_status != 'D'" PR_proteomics_experiment 13 column_length Column Length (cm) real 4 0 Y N N text 10 Y Y N "Packing length of reverse phase beads column in cm used for this experiment (Do not enter the units in the text box, just the number of cm)" PR_proteomics_experiment 14 go_public_date Go Public Date datetime 8 0 Y CURRENT_TIMESTAMP N N text 20 Y Y N Date that this experiment data will go public. Please use the form 2002-12-31. Do not enter a date higher than 2030-01-01. PR_proteomics_experiment 15 quant_normalization D0 / D8 Normalization Factor real 4 0 Y N N text 10 Y Y N "Optional Normalization factor for d0/d8 quantitation ratio. This will not be known until some data analysis has already been performed. If ratios that should be calibrated to 1:1 appear as 1.2:1, enter 1.2 here to adjust." PR_proteomics_experiment 16 pulldown_protein_name Pulldown Protein Name varchar 255 0 Y N N text 50 Y Y N "If this is a pulldown experiment, write in the bait protein here. This will permit one or more experiments to be properly visualized as a network." PR_proteomics_experiment 17 experiment_samples_ids Experiment Sample IDS varchar 255 0 Y N PR_experiments_samples experiments_samples_id N multilink 4 Y Y N Select all the Samples that were used in this experiment. "SELECT proteomics_sample_id, sample_tag FROM $TBPR_PROTEOMICS_SAMPLE WHERE record_status != 'D' ORDER BY sample_tag" PR_proteomics_experiment 18 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF PR_proteomics_experiment 19 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_proteomics_experiment 20 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_experiment 21 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_proteomics_experiment 22 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_experiment 23 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_proteomics_experiment 24 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_proteomics_experiment 25 record_status Record Status char 1 0 N N N N N PR_gradient_program 1 gradient_program_id Gradient Program ID int 4 0 N Y N N pkDEFAULT PR_gradient_program 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project to which the gradient program belongs "SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id" PR_gradient_program 3 gradient_program_name Program Name varchar 255 0 N N Y text 50 Y Y Y Title of this gradient program PR_gradient_program 4 gradient_program_description Program Description varchar 255 0 N N Y textarea 3 Y Y N One-line description of this gradient program PR_gradient_program 5 gradient_program_table Program Data text 16 0 Y N N textarea 12 Y Y N "Please enter the full gradient program here in the form of three- or four-column data. Column 1 is the time point in minutes from the beginning of the program. Column 2 and 3 are buffer A and B settings in percent. Column 4 is the flow rate in mL/min. Write no units, just the numbers. Separate with spaces." PR_gradient_program 6 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_gradient_program 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_gradient_program 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_gradient_program 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_gradient_program 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_gradient_program 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_gradient_program 12 record_status Record Status char 1 0 N N N N N PR_gradient_delta 1 gradient_delta_id Gradient Program Delta ID int 4 0 N Y N N pkDEFAULT PR_gradient_delta 2 gradient_program_id Gradient Program ID int 4 0 N N PR_gradient_program gradient_program_id Y Y Y Gradient Program of which this time point is a part PR_gradient_delta 3 gradient_delta_time Gradient Delta Time Point real 4 0 N N Y Y Y Time point in minutes as the start PR_gradient_delta 4 buffer_A_setting_percent Buffer A Setting Percent real 4 0 N N Y Y N Desired setting of Buffer A in percent (i.e. 0-100) at this timepoint PR_gradient_delta 5 buffer_B_setting_percent Buffer B Setting Percent real 4 0 N N Y Y N Desired setting of Buffer B (currently usually acetonitrile) in percent (i.e. 0-100) at this timepoint PR_gradient_delta 6 flow_rate Flow Rate (mL/min) real 4 0 N N Y Y N "Flow rate in units of mL/min (Do not write units in text box, just the number)" PR_fractionation_type 1 fractionation_type_id Fractionation Type ID int 4 0 N Y N N pkDEFAULT PR_fractionation_type 2 fractionation_type_name Fractionation Type Name varchar 100 0 N N Y text 20 Y Y Y Short name of this fractionation type as it will appear in list boxes PR_fractionation_type 3 fractionation_type_description Fractionation Type Description text 16 0 N N Y textarea 6 Y Y N More complete description of this fractionation type PR_fractionation_type 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_fractionation_type 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_fractionation_type 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_fractionation_type 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_fractionation_type 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_fractionation_type 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_fractionation_type 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_fractionation_type 11 record_status Record Status char 1 0 N N N N N PR_fraction 1 fraction_id Fraction ID int 4 0 N Y N N pkDEFAULT PR_fraction 2 experiment_id Experiment ID int 4 0 N N PR_proteomics_experiment experiment_id Y fixed Y Y Y Experiment to which this msrun belongs PR_fraction 3 fraction_tag Fraction Tag varchar 50 0 N N Y fixed Y Y Y Short tag (name) of this msrun. This corresponds to the .dat or .raw filename without the extension. Do not use spaces or non-standard characters. PR_fraction 4 fraction_number Fraction Number int 4 0 Y N N text 20 Y Y N "This corresponds to serial number of the msrun, sometimes related to the SCX fraction number, but there are no rules yet" PR_fraction 5 fraction_date Fraction Date datetime 8 0 Y N N fixed Y Y N Datetime when this msrun was completed PR_fraction 6 gradient_program_id Gradient Program ID int 4 0 Y N PR_gradient_program gradient_program_id N optionlist Y Y N Gradient Program used for this fraction "SELECT gradient_program_id,gradient_program_name FROM $TBPR_GRADIENT_PROGRAM WHERE record_status != 'D'" PR_fraction 7 column_delay Column Delay (s) int 4 0 Y N N text 20 Y Y N Column delay in seconds. This is the offset between when the pumps claims to be at a given setting and the instrument is seeing the spray at that percentage setting PR_fraction 8 fractionation_type_id Fractionation Type int 4 0 Y N PR_fractionation_type fractionation_type_id N optionlist Y Y N "Type of fractionation used to creation this fraction (SCX, FFE, etc.)" "SELECT fractionation_type_id,fractionation_type_name FROM $TBPR_FRACTIONATION_TYPE WHERE record_status != 'D'" PR_fraction 9 fraction_centroid Fraction Centroid real 4 0 Y N N text 20 Y Y N "Central value of the bin of the changing variable for this particular fraction (in salt concentration units for SCX, pI for FFE, etc.) Note that if more than one true fraction was combined, use the mean value of all the combined fractions that were actually put into the mass spec for this run" PR_fraction 10 fraction_full_width Fraction Full Width real 4 0 Y N N text 20 Y Y N "Full width of the bin of the changing variable for this particular fraction (in salt concentration units for SCX, pI for FFE, etc.) Note that if more than one true fraction was combined, use the total full width of all the combined fractions that were actually put into the mass spec in this run" PR_fraction 11 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_fraction 12 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_fraction 13 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_fraction 14 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_fraction 15 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_fraction 16 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_fraction 17 record_status Record Status char 1 0 N N N N N PR_msms_spectrum 1 msms_spectrum_id MS/MS Spectrum ID int 4 0 N Y N N pkDEFAULT PR_msms_spectrum 2 fraction_id Fraction ID int 4 0 N N PR_fraction fraction_id Y Y Y MS Run from which this spectrum comes PR_msms_spectrum 3 msms_spectrum_file_root MS/MS Spectrum File Root varchar 255 0 N N Y Y Y File root of this exactracted spectrum. This corresponds to the .dta or .out filename without the extension. Do not use spaces or non-standard characters. PR_msms_spectrum 4 start_scan Start Scan Number int 4 0 N N Y Y N Starting scan number of the MS/MS Spectrum PR_msms_spectrum 5 end_scan End Scan Number int 4 0 N N Y Y N "Ending scan number of the MS/MS Spectrum (if only a single scan, this will be the same as start_scan)" PR_msms_spectrum 6 precursor_intensity Precursor Intensity real 4 0 Y N Y Y N Mass spec intensity of the precursor peptide that is fragmented PR_msms_spectrum 7 n_peaks Number of Peaks int 4 0 N N Y Y N Number of peaks in the spectrum PR_msms_spectrum 8 spectrum_score Spectrum Score real 4 0 Y N Y Y N "Spectrum score, a floating point number of arbitrary scale" PR_msms_spectrum 9 score_version Score Version varchar 10 0 Y N Y Y N Version tag of the software used to score this spectrum PR_msms_spectrum 10 scan_time Scan Time real 4 0 Y N Y Y N Time of the start_scan in seconds after the instrument started counting PR_msms_spectrum 11 calc_buffer_percent Calculated Buffer B Percent real 4 0 Y N Y Y N Calculated percent buffer B (acetonitrile) at the time of this MS/MS spectrum PR_msms_spectrum 12 calib_buffer_percent Calibrated Buffer B Percent real 4 0 Y N Y Y N Calibrated percent buffer B (acetonitrile) at the time of this MS/MS spectrum (not used yet) PR_msms_spectrum_peak 1 msms_spectrum_id MS/MS Spectrum ID int 4 0 N N PR_msms_spectrum msms_spectrum_id Y Y Y MS/MS Spectrum to which this peak belongs PR_msms_spectrum_peak 2 mass Peak Mass float 8 0 N N Y Y Y Average mass of this peak PR_msms_spectrum_peak 3 intensity Peak Intensity real 4 0 N N Y Y N Intensity of this peak PR_biosequence_set 1 biosequence_set_id BioSequence Set ID int 4 0 N Y N N pkDEFAULT PR_biosequence_set 2 project_id Owner Project int 4 0 N N project project_id Y optionlist Y Y N Project under which this Biosequence Set is organized and for which user privileges is controlled "SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id" PR_biosequence_set 3 organism_id Organism int 4 0 N N organism organism_id Y optionlist Y Y N Organism to which the BioSequences in this database belong "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" PR_biosequence_set 4 set_name Set Name varchar 100 0 N N Y text 50 Y Y N Name of this BioSequence database PR_biosequence_set 5 set_tag Set Tag varchar 50 0 N N Y text 20 Y Y Y Short tag (name) of this BioSequence database PR_biosequence_set 6 set_description Set Description varchar 255 0 N N Y text 50 Y Y N Longer description of this BioSequence database PR_biosequence_set 7 set_version Set Version varchar 50 0 N N Y text 40 Y Y N Version of this BioSequence database PR_biosequence_set 8 polymer_type_id Polymer Type int 4 0 N N BL_polymer_type polymer_type_id Y optionlist Y Y N "Polymer type (e.g. protein, DNA, RNA) for the BioSequences in this database" "SELECT polymer_type_id, polymer_type_name FROM $TBBL_POLYMER_TYPE ORDER BY sort_order,polymer_type_name" PR_biosequence_set 9 upload_file Upload file varchar 255 0 Y N N file 40 Y Y N File path of this BioSequence database if to be uploaded via the web interface PR_biosequence_set 10 set_path Set Path varchar 255 0 N N Y text 50 Y Y N File path of this BioSequence database PR_biosequence_set 11 source_file_date Source File Date datetime 8 0 Y N N text 40 N N N Date of the FASTA file at last update PR_biosequence_set 12 uri URI varchar 255 0 Y N N text 50 Y Y N External web page or other URI SELF PR_biosequence_set 13 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_biosequence_set 14 sort_order Sort Order int 4 0 N 10 N N text 20 Y Y N Allows the ordering or ranking of Biosequence Sets which is used to break ties for choosing canonical names. Lower numbers indicate better rank. PR_biosequence_set 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence_set 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_biosequence_set 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence_set 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_biosequence_set 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_biosequence_set 20 record_status Record Status char 1 0 N N N N N PR_biosequence 1 biosequence_id BioSequence ID int 4 0 N Y N N pkDEFAULT PR_biosequence 2 biosequence_set_id BioSequence Set int 4 0 N N PR_biosequence_set biosequence_set_id N N Y BioSequence Set to which this BioSequence belongs pkDEFAULT PR_biosequence 3 biosequence_name BioSequence Name varchar 255 0 N N Y text 50 Y Y Y Name of this BioSequence (generally everything before the first space in a FASTA file header line) PR_biosequence 4 biosequence_gene_name BioSequence Gene Name varchar 255 0 Y N Y text 20 Y Y N Gene name of this BioSequence if applicable. Most common gene name if applicable PR_biosequence 5 dbxref_id Database Cross Reference int 4 0 Y N BL_dbxref dbxref_id Y Y N Database cross reference for which the accession number applies pkDEFAULT PR_biosequence 6 biosequence_accession BioSequence Accession varchar 255 0 Y N Y text 50 Y Y N Accession number for this BioSequence in some external database designated above PR_biosequence 7 organism_id Organism int 4 0 Y N organism organism_id Y optionlist Y Y N Organism to which this BioSequence belongs "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" PR_biosequence 8 polymer_type_id Polymer Type int 4 0 Y N BL_polymer_type polymer_type_id Y optionlist Y Y N "Polymer type (e.g. protein, DNA, RNA) of this BioSequence" "SELECT polymer_type_id, polymer_type_name FROM $TBBL_POLYMER_TYPE ORDER BY sort_order,polymer_type_name" PR_biosequence 9 biosequence_desc Biosequence Description varchar 1024 0 N N Y text 40 Y Y N Description of this BioSequence (generally everything after the first space in a FASTA file header line) PR_biosequence 10 biosequence_seq Sequence text 16 0 Y N N file 40 Y Y N Actual sequence of the BioSequence if known PR_biosequence 11 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_biosequence 12 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence 13 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_biosequence 14 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence 15 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_biosequence 16 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_biosequence 17 record_status Record Status char 1 0 N N N N N PR_biosequence_property_set 1 biosequence_property_set_id BioSequence Property Set ID int 4 0 N Y N N pkDEFAULT PR_biosequence_property_set 2 biosequence_id BioSequence ID int 4 0 N N PR_biosequence biosequence_id N N Y Biosequence to which this Biosequence property set belongs pkDEFAULT PR_biosequence_property_set 3 n_transmembrane_regions Number of Transmembrane Regions int 4 0 Y N Y Y N Number of transmembrane regions pkDEFAULT PR_biosequence_property_set 4 transmembrane_class Transmembrane Region Class varchar 10 0 Y N Y text 50 Y Y N "Class of the transmembrane region. May be 0, TM, A, S, TM_xS based on output from TMHMM and signalP" PR_biosequence_property_set 5 transmembrane_topology Transmembrane Region Topology varchar 1024 0 Y N Y text 20 Y Y N Coding of which residues belong in the transmembrane regions PR_biosequence_property_set 6 has_signal_peptide Has a Signal Peptide char 1 0 Y N N text 50 Y Y N "Does this protein have a signal peptide on the end Y/N? (Note that Y means that there is some non-zero probability that it does, not that is necessarily does)" PR_biosequence_property_set 7 has_signal_peptide_probability Probability that it has a Signal Peptide real 4 0 Y N N text 50 Y Y N Probability that there is a signal peptide on the end as calculated by SignalP PR_biosequence_property_set 8 signal_peptide_length Length of the Signal Peptide int 4 0 Y N N text 50 Y Y N Length in residues of the signal peptide PR_biosequence_property_set 9 signal_peptide_is_cleaved Signal Peptide gets Cleaved char 1 0 Y N N text 50 Y Y N Does the signal peptide get cleaved off Y/N? PR_biosequence_property_set 10 genome_build Genome Build varchar 50 0 Y N N text 50 Y Y N Genome build name for which the following mapping parameters are valid PR_biosequence_property_set 11 chromosome Chromosome varchar 50 0 Y N N text 50 Y Y N Chromosome in which this mapping occurs PR_biosequence_property_set 12 start_in_chromosome Start Position in Chromosome int 4 0 Y N N text 20 Y Y N Start position of the biosequence in the chromosome PR_biosequence_property_set 13 end_in_chromosome End Position in Chromosome int 4 0 Y N N text 20 Y Y N End position of the biosequence in the chromosome PR_biosequence_property_set 14 strand Strand char 1 0 Y N N text 10 Y Y N "Strand (+,-) of the biosequence in the chromosome" PR_biosequence_property_set 15 isoelectric_point Isoelectric Point real 4 0 Y N N text 10 Y Y N Isoelectric Point (pI) of the protein PR_biosequence_property_set 16 fav_codon_frequency Favorite Codon Frequency real 4 0 Y N N text 10 Y Y N Favorite Codon Frequency PR_biosequence_property_set 17 duplicate_biosequences Duplicate Biosequences varchar 255 0 Y N N text 50 Y Y N Semicolon delimited list of duplicate sequences within the same set PR_biosequence_property_set 18 category Category varchar 255 0 Y N N text 50 Y Y N Biosequence category PR_biosequence_annotation 1 biosequence_annotation_id Domain Match Type int 4 0 N Y N N pkDEFAULT PR_biosequence_annotation 2 biosequence_id BioSequence int 4 0 N N PR_biosequence biosequence_id Y fixed Y Y Y BioSequence to which this annotation belongs PR_biosequence_annotation 3 gene_symbol Gene Symbol varchar 255 0 Y N N text 50 Y Y N Gene Symbol to describe this protein (e.g. TLR2) PR_biosequence_annotation 4 full_gene_name Full Gene Name varchar 255 0 Y N N text 50 Y Y N Full name of the gene (e.g. Toll-like Receptor 2) PR_biosequence_annotation 5 aliases BioSequence Aliases varchar 255 0 Y N N text 50 Y Y N Aliases of this BioSequence. These are stored as a semi-colon delimited string PR_biosequence_annotation 6 former_names Former BioSequence Names varchar 255 0 Y N N text 50 Y Y N Former Aliases of this BioSequence. These are stored as a colon-delimited string PR_biosequence_annotation 7 functional_description Functional Description text 16 0 Y N N textarea 3 Y Y N Functional description of the protein PR_biosequence_annotation 8 EC_numbers EC Numbers varchar 255 0 Y N N text 50 Y Y N EC Number(s) that corresponds to this domain. Separate multiple numbers with a semicolon PR_biosequence_annotation 9 biosequence_type Biosequence Type varchar 255 0 Y N N text 50 Y Y N Further annotation of biosequence type PR_biosequence_annotation 10 category Category varchar 255 0 Y N N text 50 Y Y N Category PR_biosequence_annotation 11 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_biosequence_annotation 12 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence_annotation 13 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_biosequence_annotation 14 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_biosequence_annotation 15 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_biosequence_annotation 16 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_biosequence_annotation 17 record_status Record Status char 1 0 N N N N N PR_search_batch 1 search_batch_id Search Batch ID int 4 0 N Y N N pkDEFAULT PR_search_batch 2 experiment_id Experiment ID int 4 0 N N PR_proteomics_experiment experiment_id Y Y Y Y Experiment to which this search batch belongs PR_search_batch 3 biosequence_set_id BioSequence Set int 4 0 N N PR_biosequence_set biosequence_set_id Y Y Y Y BioSequence Set against which this batch was searched pkDEFAULT PR_search_batch 4 data_location Data Location varchar 255 0 N N Y text 50 Y Y N Absolute or relative location of the raw data for this search batch PR_search_batch 5 search_batch_subdir Search Batch Subdirectory varchar 100 0 N N Y text 50 Y Y Y Subdirectory under the experiment where the data for this search resides PR_search_batch_parameter 1 search_batch_id Search Batch ID int 4 0 N N PR_search_batch search_batch_id N N Y Search batch to which this search parameter belongs pkDEFAULT PR_search_batch_parameter 2 key_order Key Order int 4 0 N N Y Y Y N Monotonically increasing number to denote key order PR_search_batch_parameter 3 parameter_key Parameter Key varchar 100 0 N N Y text 50 Y Y Y The key of the key/value pair PR_search_batch_parameter 4 parameter_value Parameter Value varchar 255 0 N N Y text 50 Y Y N The value of the key/value pair PR_search_batch_parameter_set 1 search_batch_id Search Batch ID int 4 0 N Y PR_search_batch search_batch_id N N Y Search batch to which this set of search parameters belong pkDEFAULT PR_search_batch_parameter_set 2 peptide_mass_tolerance Peptide Mass Tolerance varchar 100 0 N N Y text 50 Y Y N Peptide Mass Tolerance PR_search_batch_parameter_set 3 peptide_ion_tolerance Peptide Ion Tolerance varchar 100 0 N N Y text 50 Y Y N Peptide Ion Tolerance PR_search_batch_parameter_set 4 etc and many more varchar 100 0 N N Y text 50 Y Y N This table is a an unfinished placeholder for a pivoted version of search_batch_parameter. It will be finished when it seems important to do so. PR_search 1 search_id Search ID int 4 0 N Y N N pkDEFAULT PR_search 2 search_batch_id Search Batch ID int 4 0 N N PR_search_batch search_batch_id Y fixed Y Y Y Search Batch to which this search belongs PR_search 3 msms_spectrum_id MS/MS Spectrum ID int 4 0 N N PR_msms_spectrum msms_spectrum_id Y fixed Y Y Y MS/MS Spectrum that was searched pkDEFAULT PR_search 4 file_root File Root varchar 255 0 N N Y text 50 Y Y N Root of the filename that was searched. This is usually in the format of basename.startscan.endscan.assumedcharge PR_search 5 start_scan Start Scan int 4 0 N N Y text 10 Y Y N Starting scan number PR_search 6 end_scan End Scan int 4 0 N N Y text 10 Y Y N Ending scan number PR_search 7 sample_mass_plus_H Sample (M+H)+ float 8 0 N N Y text 10 Y Y N Observed mass (M+H)+ PR_search 8 assumed_charge Assumed Charge int 4 0 N N Y text 10 Y Y N Assumed charged for this search (since charge may be unknown) PR_search 9 total_intensity Total Spectrum Intensity real 4 0 N N Y text 10 Y Y N Total intensity of the spectrum PR_search 10 matched_peptides Number of Matched Peptides int 4 0 N N Y text 10 Y Y N Number of matched peptides for this search PR_search 11 lowest_prelim_score Lowest Preliminary Score real 4 0 N N Y text 10 Y Y N Lowest preliminary score by Sequest PR_search 12 search_date Search Date datetime 8 0 N N Y text 20 Y Y N Date the the spectrum was searched PR_search 13 search_elapsed_min Search Time in Minutes real 4 0 N N Y text 10 Y Y N Length of time in minutes for the search to complete PR_search 14 search_host Search Hostname varchar 50 0 N N Y text 50 Y Y N Hostname on which the search was performed PR_search_hit 1 search_hit_id Search Hit ID int 4 0 N Y N N Search Hit ID pkDEFAULT PR_search_hit 2 search_id Search ID int 4 0 N N PR_search search_id Y Y Y Search ID to which this hit belongs PR_search_hit 3 hit_index Hit Index int 4 0 N N Y Y Y Index number of this hit to denote the order PR_search_hit 4 cross_corr_rank Cross Correlation Rank int 4 0 N N Y Y N Cross Correlation Rank PR_search_hit 5 prelim_score_rank Preliminary Score Rank int 4 0 N N Y Y N Preliminary Score Rank PR_search_hit 6 hit_mass_plus_H Hit (M+H)+ float 8 0 N N Y Y N Hit (M+H)+ PR_search_hit 7 mass_delta Mass Delta real 4 0 N N Y Y N Mass Delta PR_search_hit 8 cross_corr Cross Correlation Score real 4 0 N N Y Y N Cross Correlation Score PR_search_hit 9 norm_corr_delta Normalized Correlation Score Delta real 4 0 N N Y Y N Normalized Correlation Score Delta PR_search_hit 10 prelim_score Preliminary Score real 4 0 N N Y Y N Preliminary Score PR_search_hit 11 identified_ions Number of Identified Ions int 4 0 N N Y Y N Number of Identified Ions PR_search_hit 12 total_ions Total Number of Predicted Ions int 4 0 N N Y Y N Total Number of Predicted Ions PR_search_hit 13 reference Reference (Protein) varchar 100 0 N N Y Y N Reference (Protein) PR_search_hit 14 biosequence_id BioSequence ID int 4 0 Y N PR_biosequence biosequence_id Y Y N BioSequence ID PR_search_hit 15 best_hit_flag Best Hit Flag char 1 0 Y N Y Y N Best Hit Flag PR_search_hit 16 additional_proteins Number of Additional Proteins int 4 0 N N Y Y N Number of Additional Proteins PR_search_hit 17 peptide Peptide varchar 100 0 Y N Y Y N Peptide PR_search_hit 18 peptide_string Peptide String varchar 100 0 Y N Y Y N Peptide String PR_search_hit 19 next_dCn Next Cross Correlation Delta real 4 0 Y N Y Y N Next Cross Correlation Delta PR_search_hit 20 isoelectric_point Calculated Isoelectric Point real 4 0 Y N Y Y N Calculated Isoelectric Point PR_search_hit 21 molecular_weight Molecular Weight real 4 0 Y N Y Y N Molecular Weight PR_search_hit 22 probability Probability real 4 0 Y N Y Y N Probability PR_search_hit 23 f_score F Score real 4 0 Y N Y Y N F Score PR_search_hit 24 gravy_score Gravy Score real 4 0 Y N Y Y N Gravy Score PR_search_hit_protein 1 search_hit_protein_id Search Hit Protein ID int 4 0 N Y N N Search Hit Protein ID pkDEFAULT PR_search_hit_protein 2 search_hit_id Search Hit ID int 4 0 N N PR_search_hit search_hit_id Y Y Y Search Hit ID to which this duplicate protein belongs PR_search_hit_protein 3 reference Reference (Protein) varchar 100 0 N N Y Y Y Reference (Protein) PR_search_hit_protein 4 biosequence_id BioSequence ID int 4 0 Y N PR_biosequence biosequence_id Y Y N BioSequence ID PR_quantitation 1 quantitation_id Quantitation ID int 4 0 N Y N N Quantitation ID pkDEFAULT PR_quantitation 2 search_hit_id Search Hit ID int 4 0 N N PR_search_hit search_hit_id Y Y Y Search Hit ID PR_quantitation 3 d0_intensity d0 Intensity real 4 0 Y N Y Y N d0 Intensity PR_quantitation 4 d8_intensity d8 Intensity real 4 0 Y N Y Y N d8 Intensity PR_quantitation 5 d0_first_scan d0 First Scan int 4 0 N N Y Y N d0 First Scan PR_quantitation 6 d0_last_scan d0 Last Scan int 4 0 N N Y Y N d0 Last Scan PR_quantitation 7 d0_mass d0 Mass real 4 0 Y N Y Y N d0 Mass PR_quantitation 8 d8_first_scan d8 First Scan int 4 0 N N Y Y N d8 First Scan PR_quantitation 9 d8_last_scan d8 Last Scan int 4 0 N N Y Y N d8 Last Scan PR_quantitation 10 d8_mass d8 Mass real 4 0 Y N Y Y N d8 Mass PR_quantitation 11 norm_flag Normalization Flag int 4 0 Y N Y Y N Normalization Flag PR_quantitation 12 mass_tolerance Mass Tolerance real 4 0 Y N Y Y N Mass Tolerance PR_quantitation 13 quality_score Quality Score real 4 0 Y N Y Y N Quality Score PR_quantitation 14 manually_changed Is Manually Changed? varchar 5 0 Y N Y Y N Is Manually Changed? PR_quantitation 15 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N Date Record Created PR_quantitation 16 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N Record Created By PR_quantitation 17 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N Date Record Modified PR_quantitation 18 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N Record Modified By PR_quantitation 19 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Owner Group ID PR_quantitation 20 record_status Record Status char 1 0 N N N N N Record Status PR_search_hit_annotation 1 search_hit_annotation_id Search Hit Annotation int 4 0 N Y N N pkDEFAULT PR_search_hit_annotation 2 search_hit_id Search Hit ID int 4 0 N N PR_search_hit search_hit_id Y fixed Y Y Y Database ID for the Search Hit to be annotated PR_search_hit_annotation 3 annotation_label_id Annotation Label int 4 0 N N PR_annotation_label annotation_label_id Y scrolloptionlist 6 Y Y N Annotation label to associate with this Search Hit. A description of how sure the annotater is that this is a correct peptide identification "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_search_hit_annotation 4 annotation_confidence_id Annotation Confidence int 4 0 N N PR_annotation_confidence annotation_confidence_id Y scrolloptionlist 5 Y Y N Confidence in the above labeling "SELECT annotation_confidence_id,confidence_desc FROM $TBPR_ANNOTATION_CONFIDENCE ORDER BY sort_order,confidence_desc" PR_search_hit_annotation 5 annotation_source_id Annotation Source int 4 0 N N PR_annotation_source annotation_source_id Y fixedfromlist Y Y N Source from which this annotation came "SELECT annotation_source_id,source_desc FROM $TBPR_ANNOTATION_SOURCE ORDER BY sort_order,source_desc" PR_search_hit_annotation 6 user_annotation_label_id User-defined Annotation Label int 4 0 Y N PR_user_annotation_label user_annotation_label_id N scrolloptionlist 6 Y Y N User-defined annotation label to associate with this Search Hit. This is project-specific "SELECT user_annotation_label_id,user_annotation_tag FROM $TBPR_USER_ANNOTATION_LABEL WHERE project_id='$project_id' AND record_status !='D' ORDER BY sort_order,user_annotation_tag" PR_search_hit_annotation 7 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_search_hit_annotation 8 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_search_hit_annotation 9 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_search_hit_annotation 10 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_search_hit_annotation 11 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_search_hit_annotation 12 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_search_hit_annotation 13 record_status Record Status char 1 0 N N N N N PR_annotation_source 1 annotation_source_id Annotation Source ID int 4 0 N Y N N pkDEFAULT PR_annotation_source 2 source_desc Annotation Source Name varchar 100 0 N N Y text 50 Y Y Y Short description of this annotation source PR_annotation_source 3 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_annotation_source 4 sort_order Sort Order int 4 0 N 10 N N N N Integer that controls sorting order of the list in a list box PR_annotation_source 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_source 6 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_annotation_source 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_source 8 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_annotation_source 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_annotation_source 10 record_status Record Status char 1 0 N N N N N PR_annotation_label 1 annotation_label_id Annotation Label ID int 4 0 N Y N N pkDEFAULT PR_annotation_label 2 label_desc Annotation Label Name varchar 100 0 N N Y text 50 Y Y Y Short description of this annotation label PR_annotation_label 3 annotation_probability Annotation Probability real 4 0 Y N Y text 10 Y Y N Probability value for label PR_annotation_label 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_annotation_label 5 sort_order Sort Order int 4 0 N 10 N N N N Integer that controls sorting order of the list in a list box PR_annotation_label 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_label 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_annotation_label 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_label 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_annotation_label 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_annotation_label 11 record_status Record Status char 1 0 N N N N N PR_annotation_confidence 1 annotation_confidence_id Annotation Confidence ID int 4 0 N Y N N pkDEFAULT PR_annotation_confidence 2 confidence_desc Annotation Confidence Name varchar 100 0 N N Y text 50 Y Y Y Short description of this annotation confidence label PR_annotation_confidence 3 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_annotation_confidence 4 sort_order Sort Order int 4 0 N 10 N N N N Integer that controls sorting order of the list in a list box PR_annotation_confidence 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_confidence 6 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_annotation_confidence 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_annotation_confidence 8 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_annotation_confidence 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_annotation_confidence 10 record_status Record Status char 1 0 N N N N N PR_user_annotation_label 1 user_annotation_label_id User Annotation Label ID int 4 0 N Y N N pkDEFAULT PR_user_annotation_label 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y Y Project to which the annotation belongs "SELECT project_id, name FROM $TB_PROJECT WHERE record_status != 'D' ORDER BY name" PR_user_annotation_label 3 user_annotation_tag Annotation Tag varchar 100 0 N N Y text 20 Y Y Y Tag for this user annotation. A tag should be a short (~10 letter) name that makes this category easily recognizable in a table of data PR_user_annotation_label 4 user_annotation_desc Annotation Description varchar 255 0 N N Y text 50 Y Y N One-line description of this user annotation PR_user_annotation_label 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_user_annotation_label 6 sort_order Sort Order int 4 0 N 10 N N N N PR_user_annotation_label 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_user_annotation_label 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_user_annotation_label 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_user_annotation_label 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_user_annotation_label 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_user_annotation_label 12 record_status Record Status char 1 0 N N N N N PR_instrument_type 1 instrument_type_id Instrument Type ID int 4 0 N Y N N pkDEFAULT PR_instrument_type 2 instrument_type_name Instrument Type Name varchar 100 0 N N Y text 20 Y Y Y Short name of this instrument type as it will appear in list boxes PR_instrument_type 3 instrument_type_description Instrument Type Description varchar 255 0 N N Y text 50 Y Y N More complete description of this instrument type PR_instrument_type 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_instrument_type 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_instrument_type 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_instrument_type 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_instrument_type 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_instrument_type 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_instrument_type 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_instrument_type 11 record_status Record Status char 1 0 N N N N N PR_instrument 1 instrument_id Instrument ID int 4 0 N Y N N pkDEFAULT PR_instrument 2 instrument_type_id Instrument Type int 4 0 N N PR_instrument_type instrument_type_id Y optionlist Y Y N Type of Instrument "SELECT instrument_type_id,instrument_type_name FROM $TBPR_INSTRUMENT_TYPE ORDER BY sort_order,instrument_type_name" PR_instrument 3 instrument_name Instrument Name varchar 100 0 N N Y text 30 Y Y Y Short name of this instrument as it will appear in list boxes PR_instrument 4 instrument_description Instrument Description varchar 255 0 N N Y text 60 Y Y N More complete description of this instrument PR_instrument 5 comment Comment text 16 0 Y N N textarea 10 Y Y N Additional comments PR_instrument 6 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_instrument 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_instrument 8 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_instrument 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_instrument 10 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_instrument 11 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_instrument 12 record_status Record Status char 1 0 N N N N N PR_experiment_type 1 experiment_type_id Experiment Type ID int 4 0 N Y N N pkDEFAULT PR_experiment_type 2 experiment_type_name Experiment Type Name varchar 100 0 N N Y text 20 Y Y Y Short name of this experiment type as it will appear in list boxes PR_experiment_type 3 experiment_type_description Experiment Type Description varchar 255 0 N N Y text 50 Y Y N More complete description of this experiment type PR_experiment_type 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_experiment_type 5 sort_order Sort Order int 2 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_experiment_type 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_experiment_type 7 created_by_id Record Created By int 2 0 N 1 N contact contact_id N N PR_experiment_type 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_experiment_type 9 modified_by_id Record Modified By int 2 0 N 1 N contact contact_id N N PR_experiment_type 10 owner_group_id Owner Group ID int 2 0 N 1 N work_group work_group_id N N PR_experiment_type 11 record_status Record Status char 1 0 N N N N N PR_request_status 1 request_status_id Request Status ID int 2 0 N Y N N pkDEFAULT PR_request_status 2 request_status_name Request Status Name varchar 100 0 N N Y text 20 Y Y Y Short name of this request status as it will appear in list boxes PR_request_status 3 request_status_description Request Status Description varchar 255 0 N N Y text 50 Y Y N More complete description of this request status PR_request_status 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_request_status 5 sort_order Sort Order int 2 0 N 10 N Y text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_request_status 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_request_status 7 created_by_id Record Created By int 2 0 N 1 N contact contact_id N N PR_request_status 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_request_status 9 modified_by_id Record Modified By int 2 0 N 1 N contact contact_id N N PR_request_status 10 owner_group_id Owner Group ID int 2 0 N 1 N work_group work_group_id N N PR_request_status 11 record_status Record Status char 1 0 N N N N N PR_funding_status 1 funding_status_id Funding Status ID int 2 0 N Y N N pkDEFAULT PR_funding_status 2 funding_status_name Funding Status Name varchar 100 0 N N Y text 20 Y Y Y Short name of this funding status as it will appear in list boxes PR_funding_status 3 funding_status_description Funding Status Description varchar 255 0 N N Y text 50 Y Y N More complete description of this funding status PR_funding_status 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_funding_status 5 sort_order Sort Order int 4 0 N 10 N Y text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_funding_status 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_funding_status 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_funding_status 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_funding_status 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_funding_status 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_funding_status 11 record_status Record Status char 1 0 N N N N N PR_proteomics_experiment_request 1 experiment_request_id Experiment Request ID int 4 0 N Y N N pkDEFAULT PR_proteomics_experiment_request 2 contact_id Requesting Contact int 4 0 N N contact contact_id Y current_contact_id Y Y N Requestor of this experiment PR_proteomics_experiment_request 3 PI_contact_id PI Contact int 4 0 N N contact contact_id Y scrolloptionlist 4 Y Y N PI for this experiment "SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization" PR_proteomics_experiment_request 4 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project to which the experiment belongs "SELECT project_id, name + ' ['+budget+']' FROM $TB_PROJECT WHERE PI_contact_id='$contact_id' ORDER BY name" PR_proteomics_experiment_request 5 funding_status_id Funding Status int 4 0 N N PR_funding_status funding_status_id Y optionlist Y Y N Select the funding status for this experiment or the project with which it is associated "SELECT funding_status_id,funding_status_name FROM $TBPR_FUNDING_STATUS ORDER BY sort_order,funding_status_name" PR_proteomics_experiment_request 6 budget_number Budget Number varchar 20 0 N N Y text 20 Y Y N Budget Number which is funding this experiment. Enter NA if none. Unfunded experiments must be cleared with Dave Goodlett prior to submission PR_proteomics_experiment_request 7 experiment_name Experiment Title varchar 100 0 N N Y text 50 Y Y N Title of this experiment PR_proteomics_experiment_request 8 experiment_tag Experiment Tag varchar 20 0 N N Y text 20 Y Y Y Short tag (name) of this experiment PR_proteomics_experiment_request 9 experiment_description Experiment Description varchar 255 0 N N Y text 50 Y Y N One-line description of this experiment PR_proteomics_experiment_request 10 organism_id Sample Organism int 4 0 N N organism organism_id Y optionlist Y Y N Organism from which the sample used for this experiment was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" PR_proteomics_experiment_request 11 experiment_type_id Experiment Type int 4 0 N N PR_experiment_type experiment_type_id Y optionlist Y Y N Type of Experiment "SELECT experiment_type_id,experiment_type_name FROM $TBPR_EXPERIMENT_TYPE ORDER BY sort_order,experiment_type_name" PR_proteomics_experiment_request 12 instrument_type_id Instrument Type int 4 0 N N PR_instrument_type instrument_type_id Y optionlist Y Y N Type of Instrument "SELECT instrument_type_id,instrument_type_name FROM $TBPR_INSTRUMENT_TYPE ORDER BY sort_order,instrument_type_name" PR_proteomics_experiment_request 13 initial_search_set_id Initial Search Set int 4 0 N N PR_biosequence_set biosequence_set_id Y optionlist Y Y N Select the initial BioSequenceSet ('database') against which SEQUEST should be run "SELECT biosequence_set_id,set_path FROM $TBPR_BIOSEQUENCE_SET ORDER BY set_path" PR_proteomics_experiment_request 14 number_of_runs Number of LCMS runs varchar 50 0 N N Y text 20 Y Y N "Number of LC/MS runs for this experiment/sample (e.g., 30-50 SCX fractions is typical)" PR_proteomics_experiment_request 15 other1_contact_id Other Contact int 4 0 N N contact contact_id N scrolloptionlist 4 Y Y N You may specify another contact for this experiment. Confirmation/completion emails will be sent to this person "SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization" PR_proteomics_experiment_request 16 other2_contact_id Other Contact 2 int 4 0 N N contact contact_id N scrolloptionlist 4 Y Y N You may specify another contact for this experiment. Confirmation/completion emails will be sent to this person "SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization" PR_proteomics_experiment_request 17 request_status_id Request Status int 4 0 N N PR_request_status request_status_id Y optionlist Y Y N Status of this request "SELECT request_status_id,request_status_name FROM $TBPR_REQUEST_STATUS ORDER BY sort_order,request_status_name" PR_proteomics_experiment_request 18 comment Comment text 16 0 Y N N textarea 8 Y Y N Additional comments or notes about this submission or how the experiment should be processed PR_proteomics_experiment_request 19 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_experiment_request 20 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_proteomics_experiment_request 21 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_experiment_request 22 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_proteomics_experiment_request 23 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_proteomics_experiment_request 24 record_status Record Status char 1 0 N N N N N PR_processing_status 1 processing_status_id Processing Status ID int 4 0 N Y N N pkDEFAULT PR_processing_status 2 status_tag Status Tag varchar 50 0 N N Y text 20 Y Y Y Short tag (name) of this Status entry PR_processing_status 3 status_description Status Description varchar 255 0 N N Y text 50 Y Y N Longer description of this Status entry PR_processing_status 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_processing_status 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_processing_status 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_processing_status 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_processing_status 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_processing_status 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_processing_status 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_processing_status 11 record_status Record Status char 1 0 N N N N N PR_raw_data_file 1 raw_data_file_id Raw Data File ID int 4 0 N Y N N pkDEFAULT PR_raw_data_file 2 file_name File Name varchar 255 0 N N Y text 50 Y Y Y Name of the raw data file (no path information) PR_raw_data_file 3 file_path File Path varchar 255 0 N N Y text 50 Y Y N Current direcotory/folder path of the raw data file PR_raw_data_file 4 processing_status_id Processing Status int 4 0 N N Y optionlist Y Y N Current status of the file "SELECT processing_status_id,status_tag FROM $TBPR_PROCESSING_STATUS ORDER BY sort_order,status_tag" PR_raw_data_file 5 file_status_message File Status Message varchar 255 0 Y N N text 50 Y Y N Additional message regarding the status of the file PR_raw_data_file 6 file_written_date File Written Date datetime 8 0 Y N N text 30 Y Y N Date that the file was written PR_raw_data_file 7 file_size File Size int 4 0 Y N N text 20 Y Y N Size of the file in bytes PR_raw_data_file 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_raw_data_file 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_raw_data_file 10 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_raw_data_file 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_raw_data_file 12 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_raw_data_file 13 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_raw_data_file 14 record_status Record Status char 1 0 N N N N N PR_query_option 1 query_option_id Query Option ID int 4 0 N Y N N pkDEFAULT PR_query_option 2 option_type Option Type varchar 255 0 N N Y text 50 Y Y Y Type or category of this option PR_query_option 3 option_key Option Key varchar 255 0 N N Y text 50 Y Y Y Key for this key/value pair option PR_query_option 4 option_value Option Value varchar 255 0 Y N Y text 50 Y Y N Value of this key/value pair option PR_query_option 5 sort_order Sort Order int 4 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_query_option 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_query_option 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_query_option 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_query_option 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_query_option 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_query_option 11 record_status Record Status char 1 0 N N N N N PR_GetSearchHits 1 search_batch_id Search Batches N multioptionlist 4 Y Y N "Select desired Experiments and Search Batches to include in query. Multiple items may be selected. If no items are selected, ALL experiments are searched." MANUAL PR_GetSearchHits 2 probability_constraint Probability Constraint N text 20 Y Y N "Constraint for the probability of being the correct hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_GetSearchHits 3 annotation_status_id Annotation status constraint N optionlist Y Y N Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; leave blank to show either) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value" PR_GetSearchHits 4 annotation_label_id Annotation label constraint N multioptionlist 5 Y Y N Select desired annotation labels to include (applies only to records that have annotations) "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_GetSearchHits 5 xcorr_charge1 XCorr for +1 N text 20 Y Y N "Constraint for the XCorr value for charge state +1. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_GetSearchHits 6 xcorr_charge2 XCorr for +2 N text 20 Y Y N "Constraint for the XCorr value for charge state +2. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_GetSearchHits 7 xcorr_charge3 XCorr for +3 N text 20 Y Y N "Constraint for the XCorr value for charge state +3. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_GetSearchHits 8 delta_xcorr Delta Xcorr N text 20 Y 2 N "Constraint for the difference in XCorr between the current and next hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_GetSearchHits 9 file_root_constraint file_root Constraint N text 40 Y 2 N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 10 best_hit_constraint Best Hit Constraint N optionlist Y 1 N "Constraint for the best hit flag which is set to mark the best hit among the top ones. The best hit may not be the first one, but can be set or changed" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value" PR_GetSearchHits 11 xcorr_rank_constraint XCorr Rank Constraint N text 40 Y 2 N "Limit for the XCorr Rank value. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_GetSearchHits 12 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" PR_GetSearchHits 13 reference_constraint Reference Constraint N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 14 biosequence_accession_constraint Biosequence Accession Constraint N text 40 Y 2 N Constraint for the Biosequence Accession Number corresponding to the reference protein if there is one. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 15 description_constraint Reference Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 16 peptide_constraint Peptide Constraint N text 40 Y 2 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 17 peptide_string_constraint Peptide String Constraint N text 40 Y 2 N Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearchHits 18 peptide_options Peptide Options N multioptionlist 3 Y 1 N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value" PR_GetSearchHits 19 precursor_mass_constraint Precursor m/z constraint N text 40 Y 2 N "Constraint for the observed precursor m/z (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_GetSearchHits 20 mass_constraint Mass constraint N text 40 Y 2 N "Constraint for the theoretical peptide mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_GetSearchHits 21 start_scan_constraint Start Scan Constraint N text 40 Y 2 N "Constraint for the Start Scan value. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_GetSearchHits 22 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 2 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_GetSearchHits 23 isoelectric_point_constraint pI constraint N text 40 Y 2 N "Constraint for the isoelectric point (pI). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_GetSearchHits 24 quantitation_constraint Quantitation constraint N text 40 Y 2 N "Constraint for the Quantitation (ICAT ratio) as a single decimal value. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_GetSearchHits 25 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_sort_options' ORDER BY sort_order,option_value" PR_GetSearchHits 26 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_display_options' ORDER BY sort_order,option_value" PR_GetSearchHits 27 quantitation_values Quantitation Values N optionlist Y 1 N Specify which values to use on which side of the quantitation ratio. Normally d0/d8. Use with caution. This affects both the search constraints as well as display format "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value" PR_GetSearchHits 28 quantitation_format Quantitation Format N optionlist Y 1 N Display format for the quantitation information "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_format' ORDER BY sort_order,option_value" PR_GetSearchHits 29 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." PR_GetSearch 1 search_batch_id Search Batches N multioptionlist 4 Y Y N "Select desired Experiments and Search Batches to include in query. Multiple items may be selected. If no items are selected, ALL experiments are searched." MANUAL PR_GetSearch 2 file_root_constraint file_root Constraint N text 40 Y Y N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_GetSearch 3 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_sort_options' ORDER BY sort_order,option_value" PR_GetSearch 4 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 100 rows." PR_BrowseBioSequence 1 biosequence_set_id BioSequence Sets N multioptionlist 4 Y Y N "Select desired BioSequence Sets to include in query. Multiple items may be selected. If no items are selected, ALL sets are searched." "SELECT biosequence_set_id,set_name FROM $TBPR_BIOSEQUENCE_SET ORDER BY sort_order,set_name" PR_BrowseBioSequence 2 biosequence_name_constraint Name Constraint N text 40 Y Y N Constraint for the BioSequence Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 3 biosequence_accession_constraint Accession Constraint N text 40 Y Y N Constraint for the BioSequence Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 4 biosequence_gene_name_constraint Gene Name Constraint N text 40 Y Y N Constraint for the BioSequence Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 5 molecular_function_constraint Molecular Function Constraint N text 40 Y Y N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 6 biological_process_constraint Biological Process Constraint N text 40 Y Y N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 7 cellular_component_constraint Cellular Component Constraint N text 40 Y Y N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 8 protein_domain_constraint Protein Domain Constraint N text 40 Y Y N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 9 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y Y N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_BrowseBioSequence 10 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y Y N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_BrowseBioSequence 11 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y Y N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_BrowseBioSequence 12 biosequence_seq_constraint Sequence Constraint N text 40 Y Y N Constraint for the actual sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 13 biosequence_desc_constraint Description Constraint N text 40 Y Y N Constraint for the BioSequence Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseBioSequence 14 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value" PR_BrowseBioSequence 15 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_BrowseBioSequence 16 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value" PR_BrowseBioSequence 17 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 100 rows." PR_CompareExperiments 1 search_batch_id Search Batches N multioptionlist 4 Y Y N Select desired Experiments and Search Batches to compare. You must select at least two items. MANUAL PR_CompareExperiments 2 probability_constraint Probability Constraint N text 20 Y Y N "Constraint for the probability of being the correct hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_CompareExperiments 3 annotation_status_id Annotation status constraint N optionlist Y Y N Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value" PR_CompareExperiments 4 annotation_label_id Annotation Labels N multioptionlist 5 Y Y N Select desired annotation labels to include (applies only to records that have annotations) "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_CompareExperiments 5 xcorr_charge1 XCorr for +1 N text 20 Y Y N "Constraint for the XCorr value for charge state +1. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareExperiments 6 xcorr_charge2 XCorr for +2 N text 20 Y Y N "Constraint for the XCorr value for charge state +2. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareExperiments 7 xcorr_charge3 XCorr for +3 N text 20 Y Y N "Constraint for the XCorr value for charge state +3. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareExperiments 8 delta_xcorr Delta Xcorr N text 20 Y 2 N "Constraint for the difference in XCorr between the current and next hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareExperiments 9 file_root_constraint file_root Constraint N text 40 Y 2 N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 10 best_hit_constraint Best Hit Constraint N optionlist Y 1 N "Constraint for the best hit flag which is set to mark the best hit among the top ones. The best hit may not be the first one, but can be set or changed" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value" PR_CompareExperiments 11 xcorr_rank_constraint XCorr Rank Constraint N text 40 Y 2 N "Limit for the XCorr Rank value. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_CompareExperiments 12 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" PR_CompareExperiments 13 reference_constraint Reference N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 14 description_constraint Reference Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 15 gene_name_constraint Gene Name N text 40 Y 2 N Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 16 molecular_function_constraint GO Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 17 biological_process_constraint GO Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 18 cellular_component_constraint GO Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 19 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 20 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_CompareExperiments 21 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_CompareExperiments 22 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_CompareExperiments 23 protein_length_constraint Protein Length Constraint N text 40 Y 2 N "Constraint for the protein length. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_CompareExperiments 24 accession_constraint Accesssion Number N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 25 peptide_constraint Peptide Constraint N text 40 Y 1 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 26 peptide_string_constraint Peptide String Constraint N text 40 Y 2 N Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareExperiments 27 peptide_options Peptide Options N multioptionlist 3 Y 1 N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value" PR_CompareExperiments 28 precursor_mass_constraint Precursor Mass constraint N text 40 Y 1 N "Constraint for the measured precursor mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareExperiments 29 mass_constraint Mass constraint N text 40 Y 2 N "Constraint for the theoretical peptide mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareExperiments 30 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 2 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareExperiments 31 isoelectric_point_constraint pI constraint N text 40 Y 2 N "Constraint for the theoretical isoelectric point (pI). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareExperiments 32 quantitation_values Quantitation Values N optionlist Y 1 N Specify which values to use on which side of the quantitation ratio. Normally d0/d8. Use with caution. This affects both the search constraints as well as display format "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value" PR_CompareExperiments 33 quantitation_constraint Quantitation constraint N text 40 Y 2 N "Constraint for the Quantitation (ICAT ratio) as a single decimal value. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareExperiments 34 n_annotations_constraint # of matches constraint N text 10 Y 2 N "Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_CompareExperiments 35 n_in_column_1_constraint # in Experiment 1 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 1 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 36 n_in_column_2_constraint # in Experiment 2 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 2 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 37 n_in_column_3_constraint # in Experiment 3 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 3 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 38 n_in_column_4_constraint # in Experiment 4 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 4 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 39 n_in_column_5_constraint # in Experiment 5 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 5 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 40 n_in_column_6_constraint # in Experiment 6 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 6 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareExperiments 41 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CE_sort_options' ORDER BY sort_order,option_value" PR_CompareExperiments 42 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_CompareExperiments 43 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value" PR_CompareExperiments 44 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." PR_CompareMSRuns 1 search_batch_id Search Batches N multioptionlist 4 refreshDocument() Y Y N Select desired Experiments and Search Batches to compare. You must select at least two items. MANUAL PR_CompareMSRuns 2 fraction_id MS Runs N multioptionlist 4 Y Y N Select desired MS Runs to compare. You must select at least two items. MANUAL PR_CompareMSRuns 3 probability_constraint Probability Constraint N text 20 Y Y N "Constraint for the probability of being the correct hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_CompareMSRuns 4 annotation_status_id Annotation status constraint N optionlist Y Y N Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value" PR_CompareMSRuns 5 annotation_label_id Annotation Labels N multioptionlist 5 Y Y N Select desired annotation labels to include (applies only to records that have annotations) "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_CompareMSRuns 6 xcorr_charge1 XCorr for +1 N text 20 Y Y N "Constraint for the XCorr value for charge state +1. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareMSRuns 7 xcorr_charge2 XCorr for +2 N text 20 Y Y N "Constraint for the XCorr value for charge state +2. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareMSRuns 8 xcorr_charge3 XCorr for +3 N text 20 Y Y N "Constraint for the XCorr value for charge state +3. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareMSRuns 9 delta_xcorr Delta Xcorr N text 20 Y 2 N "Constraint for the difference in XCorr between the current and next hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_CompareMSRuns 10 file_root_constraint file_root Constraint N text 40 Y 2 N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 11 best_hit_constraint Best Hit Constraint N optionlist Y 1 N "Constraint for the best hit flag which is set to mark the best hit among the top ones. The best hit may not be the first one, but can be set or changed" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value" PR_CompareMSRuns 12 xcorr_rank_constraint XCorr Rank Constraint N text 40 Y 2 N "Limit for the XCorr Rank value. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_CompareMSRuns 13 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" PR_CompareMSRuns 14 reference_constraint Reference N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 15 description_constraint Reference Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 16 gene_name_constraint Gene Name N text 40 Y 2 N Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 17 molecular_function_constraint GO Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 18 biological_process_constraint GO Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 19 cellular_component_constraint GO Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 20 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 21 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_CompareMSRuns 22 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_CompareMSRuns 23 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_CompareMSRuns 24 protein_length_constraint Protein Length Constraint N text 40 Y 2 N "Constraint for the protein length. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_CompareMSRuns 25 accession_constraint Accesssion Number N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 26 peptide_constraint Peptide Constraint N text 40 Y 1 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 27 peptide_string_constraint Peptide String Constraint N text 40 Y 2 N Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareMSRuns 28 peptide_options Peptide Options N multioptionlist 3 Y 1 N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value" PR_CompareMSRuns 29 precursor_mass_constraint Precursor Mass constraint N text 40 Y 1 N "Constraint for the measured precursor mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareMSRuns 30 mass_constraint Mass constraint N text 40 Y 2 N "Constraint for the theoretical peptide mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareMSRuns 31 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 2 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareMSRuns 32 isoelectric_point_constraint pI constraint N text 40 Y 2 N "Constraint for the theoretical isoelectric point (pI). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareMSRuns 33 quantitation_values Quantitation Values N optionlist Y 1 N Specify which values to use on which side of the quantitation ratio. Normally d0/d8. Use with caution. This affects both the search constraints as well as display format "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value" PR_CompareMSRuns 34 quantitation_constraint Quantitation constraint N text 40 Y 2 N "Constraint for the Quantitation (ICAT ratio) as a single decimal value. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareMSRuns 35 n_annotations_constraint # of matches constraint N text 10 Y 2 N "Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_CompareMSRuns 36 n_in_column_1_constraint # in Experiment 1 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 1 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 37 n_in_column_2_constraint # in Experiment 2 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 2 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 38 n_in_column_3_constraint # in Experiment 3 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 3 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 39 n_in_column_4_constraint # in Experiment 4 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 4 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 40 n_in_column_5_constraint # in Experiment 5 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 5 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 41 n_in_column_6_constraint # in Experiment 6 constraint N text 10 Y 2 N "Constraint for the number of entries per row for experiment 6 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareMSRuns 42 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CE_sort_options' ORDER BY sort_order,option_value" PR_CompareMSRuns 43 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_CompareMSRuns 44 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value" PR_CompareMSRuns 45 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." PR_CompareBySpectrum 1 search_batch_id Search Batches N multioptionlist 4 Y Y N Select desired Experiments and Search Batches to compare. You must select at least two items. MANUAL PR_CompareBySpectrum 2 probability_constraint Overall Probability Constraint N text 20 Y Y N "Constraint for the overall probability for all values in the query of being the correct hit. Careful about how this may conflict with the probability settings below. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_CompareBySpectrum 3 file_root_constraint file_root Constraint N text 40 Y Y N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_CompareBySpectrum 4 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" PR_CompareBySpectrum 5 precursor_mass_constraint Precursor Mass constraint N text 40 Y 1 N "Constraint for the measured precursor mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareBySpectrum 6 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 1 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_CompareBySpectrum 7 probability_in_column_1_constraint Probability in Experiment 1 constraint N text 10 Y Y N "Constraint for the probability for search batch 1 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 8 probability_in_column_2_constraint Probability in Experiment 2 constraint N text 10 Y Y N "Constraint for the probability for search batch 2 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 9 probability_in_column_3_constraint Probability in Experiment 3 constraint N text 10 Y Y N "Constraint for the probability for search batch 3 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 10 probability_in_column_4_constraint Probability in Experiment 4 constraint N text 10 Y Y N "Constraint for the probability for search batch 4 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 11 probability_in_column_5_constraint Probability in Experiment 5 constraint N text 10 Y Y N "Constraint for the probability for search batch 5 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 12 probability_in_column_6_constraint Probability in Experiment 6 constraint N text 10 Y Y N "Constraint for the probability for search batch 6 (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n""" PR_CompareBySpectrum 13 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CBS_display_options' ORDER BY sort_order,option_value" PR_CompareBySpectrum 14 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." PR_SummarizePeptides 1 search_batch_id Search Batches N multioptionlist 4 Y Y N Select desired Experiments and Search Batches to include in query. Multiple items may be selected. At least one must be selected MANUAL PR_SummarizePeptides 2 probability_constraint Probability Constraint N text 20 Y Y N "Constraint for the probability of being the correct hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_SummarizePeptides 3 annotation_status_id Annotation status constraint N optionlist Y Y N Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value" PR_SummarizePeptides 4 annotation_label_id Annotation Labels N multioptionlist 5 Y Y N Select desired annotation labels to include (applies only to records that have annotations) "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_SummarizePeptides 5 xcorr_charge1 XCorr for +1 N text 20 Y Y N "Constraint for the XCorr value for charge state +1. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_SummarizePeptides 6 xcorr_charge2 XCorr for +2 N text 20 Y Y N "Constraint for the XCorr value for charge state +2. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_SummarizePeptides 7 xcorr_charge3 XCorr for +3 N text 20 Y Y N "Constraint for the XCorr value for charge state +3. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_SummarizePeptides 8 delta_xcorr Delta Xcorr N text 20 Y 2 N "Constraint for the difference in XCorr between the current and next hit. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n""" PR_SummarizePeptides 9 file_root_constraint file_root Constraint N text 40 Y 2 N Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 10 best_hit_constraint Best Hit Constraint N optionlist Y 1 N "Constraint for the best hit flag which is set to mark the best hit among the top ones. The best hit may not be the first one, but can be set or changed" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value" PR_SummarizePeptides 11 xcorr_rank_constraint XCorr Rank Constraint N text 40 Y 2 N "Limit for the XCorr Rank value. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_SummarizePeptides 12 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" PR_SummarizePeptides 13 reference_constraint Reference N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 14 description_constraint Reference Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 15 gene_name_constraint Gene Name N text 40 Y 2 N Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 16 molecular_function_constraint Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 17 biological_process_constraint Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 18 cellular_component_constraint Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 19 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 20 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_SummarizePeptides 21 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_SummarizePeptides 22 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_SummarizePeptides 23 accession_constraint Accesssion Number N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 24 peptide_constraint Peptide N text 40 Y 2 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 25 peptide_string_constraint Peptide String Constraint N text 40 Y 2 N Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_SummarizePeptides 26 peptide_options Peptide Options N multioptionlist 3 Y 1 N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value" PR_SummarizePeptides 27 precursor_mass_constraint Precursor Mass constraint N text 40 Y 1 N "Constraint for the measured precursor mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_SummarizePeptides 28 mass_constraint Mass constraint N text 40 Y 2 N "Constraint for the theoretical peptide mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_SummarizePeptides 29 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 2 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_SummarizePeptides 30 isoelectric_point_constraint pI constraint N text 40 Y 2 N "Constraint for the theoretical isoelectric point (pI). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_SummarizePeptides 31 quantitation_values Quantitation Values N optionlist Y 1 N Specify which values to use on which side of the quantitation ratio. Normally d0/d8. Use with caution. This affects both the search constraints as well as display format "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value" PR_SummarizePeptides 32 quantitation_constraint Quantitation constraint N text 40 Y 2 N "Constraint for the Quantitation (ICAT ratio) as a single decimal value. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_SummarizePeptides 33 n_annotations_constraint # of matches constraint N text 10 Y 2 N "Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match) Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_SummarizePeptides 34 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_sort_options' ORDER BY sort_order,option_value" PR_SummarizePeptides 35 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_SummarizePeptides 36 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value" PR_SummarizePeptides 37 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 5000 rows." PR_SummarizeFractions 1 experiment_id Experiments N multioptionlist 4 Y Y N Select desired Experiments to include in query. Multiple items may be selected. At least one must be selected MANUAL PR_SummarizeFractions 2 project_id Project N multioptionlist 4 Y Y N Project in which to search for experiments MANUAL PR_SummarizeFractions 3 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 1000 rows." PR_protein_summary 1 protein_summary_id Protein Summary ID int 4 0 N Y pkDEFAULT PR_protein_summary 2 execution_date Execution Date datetime 8 0 Y N PR_protein_summary 3 program_version Program Version Number varchar 255 0 Y N PR_protein_summary 4 summary_xml Summary XML varchar 255 0 Y N PR_protein_summary_header 1 protein_summary_header_id Protein Summary Header ID int 4 0 N Y pkDEFAULT PR_protein_summary_header 2 protein_summary_id Protein Summary int 4 0 N N PR_protein_summary protein_summary_id PR_protein_summary_header 3 reference_database Reference Database varchar 255 0 N N PR_protein_summary_header 4 residue_substitution_list Residue Substitution List varchar 255 0 N N PR_protein_summary_header 5 enzyme Digestion Enzyme varchar 100 0 Y N PR_protein_summary_header 6 occam_flag Occam Flag char 1 0 Y N PR_protein_summary_header 7 groups_flag Groups Flag char 1 0 Y N PR_protein_summary_header 8 degen_flag Degeneracy Flag char 1 0 Y N PR_protein_summary_header 9 nsp_flag N Sibling Peptides Flag char 1 0 Y N PR_protein_summary_header 10 source_files Source Files text 16 0 Y N PR_protein_summary_header 11 min_peptide_probability Minimum Peptide Probability real 4 0 N N PR_protein_summary_header 12 min_peptide_weight Minimum Peptide Weight real 4 0 N N PR_protein_summary_data_filter 1 protein_summary_data_filter_id Protein Summary Data Filter ID int 4 0 N Y pkDEFAULT PR_protein_summary_data_filter 2 protein_summary_header_id Protein Summary Header ID int 4 0 N N PR_protein_summary_header protein_summary_header_id PR_protein_summary_data_filter 3 min_probability Minimum Probability real 4 0 N N PR_protein_summary_data_filter 4 sensitivity Sensitivity real 4 0 N N PR_protein_summary_data_filter 5 false_positive_error_rate False Positive Error Rate real 4 0 N N PR_nsp_information 1 nsp_information_id NSP Information ID int 4 0 N Y pkDEFAULT PR_nsp_information 2 protein_summary_header_id Protein Summary Header ID int 4 0 N N PR_protein_summary_header protein_summary_header_id PR_nsp_information 3 neighboring_bin_smoothing Neighboring Bin Smoothing char 1 0 N N PR_nsp_distribution 1 nsp_distribution_id NSP Distribution ID int 4 0 N Y pkDEFAULT PR_nsp_distribution 2 nsp_information_id NSP Information ID int 4 0 N N PR_nsp_information nsp_information_id PR_nsp_distribution 3 bin_no Neighboring Bin Smoothing char 1 0 N N PR_nsp_distribution 4 nsp_lower_bound_incl NSP Lower Bound Inclusive real 4 0 N N PR_nsp_distribution 5 nsp_upper_bound_excl NSP Upper Bound Exlusive real 4 0 N N PR_nsp_distribution 6 pos_freq Positive Frequency real 4 0 N N PR_nsp_distribution 7 neg_freq Negative Frequency real 4 0 N N PR_nsp_distribution 8 pos_to_neg_ratio Positive to Negative Frequencies Ratio real 4 0 N N PR_summary_quantitation 1 summary_quantitation_id Summary Quantitation ID int 4 0 N Y pkDEFAULT PR_summary_quantitation 2 ratio_mean Ratio Mean real 4 0 N N PR_summary_quantitation 3 ratio_standard_dev Ratio Standard Deviation real 4 0 N N PR_summary_quantitation 4 ratio_number_peptides Number of Peptides in Mean int 4 0 Y N PR_protein_group 1 protein_group_id Protein Group ID int 4 0 N Y pkDEFAULT PR_protein_group 2 protein_summary_id Protein Summary int 4 0 N N PR_protein_summary protein_summary_id PR_protein_group 3 group_number Group Number int 4 0 N N PR_protein_group 4 pseudo_name Group Pseudoname varchar 255 0 Y N PR_protein_group 6 probability Probability real 4 0 Y N PR_protein_group 7 summary_quantitation_id Summary Quantitation int 4 0 Y N PR_summary_quantitation summary_quantitation_id PR_protein 1 protein_id Protein ID int 4 0 N Y pkDEFAULT PR_protein 2 protein_group_id Protein Group int 4 0 N N PR_protein_group protein_group_id PR_protein 3 protein_name Protein Name varchar 255 0 N N PR_protein 5 probability Probability real 4 0 N N PR_protein 6 percent_coverage Percent Coverage real 4 0 Y N PR_protein 7 n_indistinguishable_proteins Number of Indistinguishable Proteins int 4 0 Y N PR_protein 8 biosequence_id Biosequence ID int 4 0 N N PR_protein 9 summary_quantitation_id Summary Quantitation int 4 0 Y N PR_summary_quantitation summary_quantitation_id PR_protein 10 n_peptides Number of Peptides int 4 0 Y N PR_indistinguishable_protein 1 indistinguishable_protein_id Indistinguishable Protein ID int 4 0 N Y pkDEFAULT PR_indistinguishable_protein 2 protein_id Lead Protein int 4 0 N N PR_protein protein_id PR_indistinguishable_protein 3 protein_name Protein Name varchar 255 0 N N PR_indistinguishable_protein 4 biosequence_id Biosequence ID int 4 0 N N PR_peptide 1 peptide_id Peptide ID int 4 0 N Y pkDEFAULT PR_peptide 2 protein_id Protein int 4 0 N N PR_protein protein_id PR_peptide 3 peptide_sequence Peptide Sequence varchar 255 0 N N PR_peptide 4 charge Charge int 4 0 N N PR_peptide 6 initial_probability Initial Probability real 4 0 N N PR_peptide 7 nsp_adjusted_probability NSP Adjusted Probability real 4 0 N N PR_peptide 8 peptide_group_designator Peptide Twin Designator varchar 10 0 Y N PR_peptide 9 weight Weight real 4 0 N N PR_peptide 10 is_nondegenerate_evidence Is Nondegenerate Evidence? char 1 0 N N PR_peptide 11 n_enzymatic_termini Number of Enzymatic Termini int 4 0 N N PR_peptide 12 n_sibling_peptides Number of Sibling Peptides real 4 0 Y N PR_peptide 13 n_sibling_peptides_bin Number of Sibling Peptides Bin int 4 0 N N PR_peptide 14 n_instances Number of Observed Instances int 4 0 N N PR_peptide 15 summary_quantitation_id Summary Quantitation int 4 0 Y N PR_summary_quantitation summary_quantitation_id PR_peptide_parent_protein 1 peptide_parent_protein_id Peptide Parent Protein ID int 4 0 N Y pkDEFAULT PR_peptide_parent_protein 2 peptide_id Peptide int 4 0 N N PR_peptide peptide_id PR_peptide_parent_protein 3 protein_name Protein Name varchar 255 0 N N PR_peptide_parent_protein 4 biosequence_id Biosequence ID int 4 0 N N PR_indistinguishable_peptide 1 indistinguishable_peptide_id Indistinguishable Peptide ID int 4 0 N Y pkDEFAULT PR_indistinguishable_peptide 2 peptide_id Peptide int 4 0 N N PR_peptide peptide_id PR_indistinguishable_peptide 3 peptide_sequence Peptide Sequence varchar 255 0 N N PR_search_batch_protein_summary 1 search_batch_protein_summary_id Search Batch Protein Summary ID int 4 0 N Y pkDEFAULT PR_search_batch_protein_summary 2 protein_summary_id Protein Summary int 4 0 N N PR_protein_summary protein_summary_id PR_search_batch_protein_summary 3 search_batch_id Search Batch ID int 4 0 N N PR_search_batch search_batch_id Y fixed Y Y Y Search Batch to which this summary belongs PR_search_batch_protein_summary 4 comment Comment text 16 0 Y N PR_possible_peptide 1 possible_peptide_id Possible Peptide ID int 4 0 N Y pkDEFAULT PR_possible_peptide 2 biosequence_id BioSequence ID int 4 0 Y N PR_biosequence biosequence_id Y Y N BioSequence ID PR_possible_peptide 3 mass Mass real 4 0 Y N PR_possible_peptide 4 peptide_sequence Peptide Sequence varchar 255 0 N N PR_possible_peptide 5 peptide_offset Peptide Offset int 4 0 N N PR_possible_peptide 6 preceding_residue Preceding Residue char 1 0 N N PR_possible_peptide 7 following_residue Following Residue char 1 0 N N PR_possible_peptide 8 n_tryptic_terminii Number of Tryptic Termini int 4 0 N N PR_possible_peptide 9 is_cysteine_containing Is Cytsteine Containing char 1 0 N N PR_possible_peptide 10 is_unique Is Unique char 1 0 N N PR_possible_peptide 11 isoelectric_point Isoelectric Point real 4 0 Y N PR_possible_peptide 12 elution_index Elution Index real 4 0 Y N PR_BrowsePossiblePeptides 1 biosequence_set_id BioSequence Sets N multioptionlist 4 Y Y N "Select desired BioSequence Sets to include in query. Multiple items may be selected. If no items are selected, ALL sets are searched." "SELECT biosequence_set_id,set_name FROM $TBPR_BIOSEQUENCE_SET ORDER BY sort_order,set_name" PR_BrowsePossiblePeptides 2 biosequence_name_constraint Name Constraint N text 40 Y Y N Constraint for the BioSequence Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 3 biosequence_gene_name_constraint Gene Name Constraint N text 40 Y Y N Constraint for the BioSequence Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 4 accession_constraint Accesssion Number N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 5 biosequence_seq_constraint Sequence Constraint N text 40 Y Y N Constraint for the actual sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 6 biosequence_desc_constraint Description Constraint N text 40 Y Y N Constraint for the BioSequence Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 7 molecular_function_constraint Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 8 biological_process_constraint Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 9 cellular_component_constraint Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 10 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 11 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_BrowsePossiblePeptides 12 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_BrowsePossiblePeptides 13 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_BrowsePossiblePeptides 14 protein_length_constraint Protein Length Constraint N text 40 Y 2 N "Constraint for the protein length. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_BrowsePossiblePeptides 15 peptide_constraint Peptide Constraint N text 40 Y 1 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowsePossiblePeptides 16 mass_constraint Mass Constraint N text 40 Y 2 N "Constraint for the theoretical peptide mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_BrowsePossiblePeptides 17 isoelectric_point_constraint Isoelectric Point Constraint N text 40 Y 2 N "Constraint for the theoretical peptide pI (isoelectric point). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_BrowsePossiblePeptides 18 n_occurrences Number of Occurrences N text 15 Y 1 N "Constraint for the number of entries per row (only applicable for one of the two Grouping options) Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n""" PR_BrowsePossiblePeptides 19 peptide_options Peptide Options N multioptionlist 3 Y Y N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPP_peptide_options' ORDER BY sort_order,option_value" PR_BrowsePossiblePeptides 20 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_BrowsePossiblePeptides 21 display_options Display Options N multioptionlist 3 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPP_display_options' ORDER BY sort_order,option_value" PR_BrowsePossiblePeptides 22 row_limit Maximum Rows N text 10 Y Y N "Limit the numbers of rows displayed. If not provided, default is 100 rows." PR_publication_category 1 publication_category_id Publication Category ID int 4 0 N Y N N pkDEFAULT PR_publication_category 2 publication_category_name Publication Category Name varchar 100 0 N N Y text 40 Y Y Y Short name of this category as it will appear in list boxes PR_publication_category 3 publication_category_description Publication Category Description varchar 255 0 N N Y text 50 Y Y N More complete description of this publication category PR_publication_category 4 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_publication_category 5 sort_order Sort Order int 2 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_publication_category 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication_category 7 created_by_id Record Created By int 2 0 N 1 N contact contact_id N N PR_publication_category 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication_category 9 modified_by_id Record Modified By int 2 0 N 1 N contact contact_id N N PR_publication_category 10 owner_group_id Owner Group ID int 2 0 N 1 N work_group work_group_id N N PR_publication_category 11 record_status Record Status char 1 0 N N N N N PR_publication_rating 1 publication_rating_id Publication Rating ID int 4 0 N Y N N pkDEFAULT PR_publication_rating 2 publication_rating_number Publication Rating Number int 4 0 N N Y text 10 Y Y Y Numerical rating of the paper on a scale of 1-10 PR_publication_rating 3 publication_rating_name Publication Rating Name varchar 100 0 N N Y text 40 Y Y Y Short name of this rating level as it will appear in list boxes PR_publication_rating 4 publication_rating_description Publication Rating Description varchar 255 0 N N Y text 50 Y Y N More complete description of this rating level PR_publication_rating 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_publication_rating 6 sort_order Sort Order int 2 0 N 10 N N text 10 Y Y N Numbers which override alphabetical sorting in a list box PR_publication_rating 7 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication_rating 8 created_by_id Record Created By int 2 0 N 1 N contact contact_id N N PR_publication_rating 9 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication_rating 10 modified_by_id Record Modified By int 2 0 N 1 N contact contact_id N N PR_publication_rating 11 owner_group_id Owner Group ID int 2 0 N 1 N work_group work_group_id N N PR_publication_rating 12 record_status Record Status char 1 0 N N N N N PR_publication 1 publication_id Publication ID int 8 0 N Y N N pkDEFAULT PR_publication 2 pubmed_ID PubMed ID varchar 50 0 Y N N text 30 refreshDocument() Y Y N "PubMed ID for this publication. When this field is changed, the interface fetch the title,author,etc. information for you if the field below this (Publication Name) is empty" PR_publication 3 publication_name Publication Name varchar 255 0 N N Y text 50 Y Y Y "Friendly name of the citation, e.g. Dewey, Cheetham & Howe (1998)" PR_publication 4 keywords Keywords varchar 255 0 Y N N text 50 Y Y N A comma-separated list of keywords appropriate when searching for papers of this sort PR_publication 5 publication_category_id Publication Category int 4 0 Y N PR_publication_category publication_category_id N optionlist Y Y N Broad category within which this publication is classified "SELECT publication_category_id,publication_category_name FROM $TBPR_PUBLICATION_CATEGORY WHERE record_status != 'D' ORDER BY sort_order,publication_category_name" PR_publication 6 publication_rating_id Publication Rating int 4 0 Y N PR_publication_rating publication_rating_id N optionlist Y Y N Rating of this paper (typically within the category) given by the person entering this record. This should be an indication of how worthwhile a read this paper is within the category "SELECT publication_rating_id,STR(publication_rating_number,5,0)+' - '+publication_rating_name FROM $TBPR_PUBLICATION_RATING WHERE record_status != 'D' ORDER BY sort_order,publication_rating_number DESC,publication_rating_name" PR_publication 7 presented_on_date Presented Date datetime 8 0 Y N N text 20 Y Y N Date that the publication was presented in a journal club PR_publication 8 presented_by_contact_id Presented By Contact int 4 0 Y N contact contact_id N scrolloptionlist 4 Y Y N Person who presented this paper in a journal club "SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization" PR_publication 9 title Title varchar 255 0 Y N N textarea 2 Y Y N Title of the article PR_publication 10 author_list Author List varchar 255 0 Y N N textarea 2 Y Y N "Author list in 'Lastname, FIMI' format" PR_publication 11 journal_name Journal Name varchar 100 0 Y N N text 50 Y Y N Name of the Journal in which the article appears PR_publication 12 published_year Published Year varchar 10 0 Y N N text 20 Y Y N Year the article was published PR_publication 13 volume_number Volume Number varchar 50 0 Y N N text 20 Y Y N Volume number of the article PR_publication 14 issue_number Issue Number varchar 50 0 Y N N text 20 Y Y N Issue number of the article PR_publication 15 page_numbers Page Numbers varchar 50 0 Y N N text 30 Y Y N Page numbers of the article PR_publication 16 publisher_name Publisher Name varchar 255 0 Y N N text 40 Y Y N Name of the publisher PR_publication 17 editor_name Editor Name varchar 255 0 Y N N text 40 Y Y N "Name of the editor, if any" PR_publication 18 uri URI varchar 255 0 Y N N text 50 Y Y N "URL of other locator for the article, either out on the Internet or in the location Publications repository" SELF PR_publication 19 abstract Abstract text 16 0 Y N N textarea 4 Y Y N Plain text abstract of the article PR_publication 20 full_manuscript_file Manuscript File Upload varchar 255 0 Y N N file 40 Y Y N Actual file containing the manuscript (e.g. in PDF format) uploaded_file PR_publication 21 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments PR_publication 22 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication 23 created_by_id Record Created By int 8 0 N N contact contact_id N N PR_publication 24 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_publication 25 modified_by_id Record Modified By int 8 0 N N contact contact_id N N PR_publication 26 owner_group_id Owner Group ID int 8 0 N 1 N work_group work_group_id N N PR_publication 27 record_status Record Status char 1 0 N N N N N PR_BrowseProteinSummary 1 search_batch_id Search Batches N multioptionlist 4 Y Y N Select desired Experiments and Search Batches to include in query. Multiple items may be selected. At least one must be selected MANUAL PR_BrowseProteinSummary 2 protein_group_probability_constraint Protein Group Probability Constraint N text 20 Y Y N "Constraint for the probability of the protein group being present in the sample. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_BrowseProteinSummary 3 protein_probability_constraint Protein Probability Constraint N text 20 Y Y N "Constraint for the probability of the protein being present in the sample. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_BrowseProteinSummary 4 annotation_status_id Annotation status Constraint N optionlist Y Y N Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value" PR_BrowseProteinSummary 5 annotation_label_id Annotation Labels Constraint N multioptionlist 5 Y Y N Select desired annotation labels to include (applies only to records that have annotations) "SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc" PR_BrowseProteinSummary 6 reference_constraint Protein Name Constraint N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 7 description_constraint Protein Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 8 gene_name_constraint Gene Name Constraint N text 40 Y 2 N Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 9 molecular_function_constraint Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 10 biological_process_constraint Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 11 cellular_component_constraint Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 12 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 13 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" PR_BrowseProteinSummary 14 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" PR_BrowseProteinSummary 15 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" PR_BrowseProteinSummary 16 accession_constraint Accesssion Number Constraint N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. PR_BrowseProteinSummary 17 quantitation_constraint Quantitation constraint N text 40 Y 2 N "Constraint for the Quantitation (ICAT ratio) as a single decimal value. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" PR_BrowseProteinSummary 18 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" PR_BrowseProteinSummary 19 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPS_display_options' ORDER BY sort_order,option_value" PR_BrowseProteinSummary 20 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 5000 rows." PR_proteomics_sample 1 proteomics_sample_id Proteomics Sample ID int 4 0 N Y Y N N Y Proteomics Sample ID pkDEFAULT PR_proteomics_sample 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y N FK to project.project_id "SELECT project_id, UL.username + ' - ' + proj.name + ' ( ' + RTRIM(CAST(proj.project_id AS CHAR)) + ' )' AS name FROM $TB_PROJECT proj JOIN $TB_USER_LOGIN UL ON (proj.PI_contact_id = UL.contact_id) WHERE proj.project_tag IS NOT NULL AND proj.record_status != 'D' ORDER BY UL.username" PR_proteomics_sample 3 sample_tag Sample Tag varchar 50 0 N N Y text 50 Y Y N Sample Name. Keep it short. Do not use any strange characters like /\*&$() (e.g. NP Epi 03-123) PR_proteomics_sample 4 full_sample_name Full Sample Name varchar 255 0 Y N Y textarea 3 Y Y N "Full Sample Name. A longer, less cryptic name should be placed here. It should be long enough so that someone else can understand quickly the general idea of the sample. (e.g. Epithelial cells FACS sorted from ""normal"" prostate tissue from specimen 03-123)" PR_proteomics_sample 5 sample_group_name Sample Group Name varchar 50 0 Y N N text 50 Y Y N Sample Group Name. Name used to group together biological replicates PR_proteomics_sample 6 sample_provider_organization_id Sample Provider int 4 0 Y N organization organization_id N optionlist Y Y N "Provider of this biomaterial (academic department, research lab, vendor, etc.)" "SELECT O.organization_id,O.organization FROM $TB_ORGANIZATION O INNER JOIN $TB_ORGANIZATION_TYPE OT ON (O.organization_type_id=OT.organization_type_id) WHERE O.record_status != 'D' ORDER BY organization" PR_proteomics_sample 7 organism_id Organism int 4 0 Y N organism organism_id N optionlist Y Y N Organism from which the biomaterial was derived "SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name" PR_proteomics_sample 8 strain_or_line Strain or Line varchar 255 0 Y N N text 50 Y Y N Strain or line of the individual PR_proteomics_sample 9 individual Individual varchar 255 0 Y N N text 50 Y Y N Identifier or name of the individual organism from which the biomaterial was derived PR_proteomics_sample 10 sex_ontology_term_id Sex int 4 0 Y N N optionlist Y Y N Sex of the individual "SELECT MOT2.MGED_ontology_term_id,MOT2.name FROM $TB_MGED_ONTOLOGY_RELATIONSHIP MOR INNER JOIN $TB_MGED_ONTOLOGY_TERM MOT2 ON ( MOR.subject_term_id = MOT2.MGED_ontology_term_id ) WHERE MOR.object_term_id = 5497 ORDER BY MOT2.name" PR_proteomics_sample 11 age Age varchar 255 0 Y N N text 50 Y Y N "Age of the individual at the time of harvest of the biomaterial. Free form text; include units, developmental stage, and reference point as appropriate (e.g., days since planting, years after birth, minutes after death)" PR_proteomics_sample 12 organism_part Organism Part varchar 255 0 Y N N text 50 Y Y N "Part of the organism's anatomy from the biomaterial was derived, excludes cells. (e.g., tissue, organ, system, or body location)" PR_proteomics_sample 13 cell_line Cell Line varchar 255 0 Y N N text 50 Y Y N Identifier for the cell line if one was used as a biomaterial PR_proteomics_sample 14 cell_type Cell Type varchar 255 0 Y N N text 50 Y Y N "Type of cell used as the biomaterial (e.g., epithelial, glial, etc.)" PR_proteomics_sample 15 disease_state Disease State varchar 255 0 Y N N text 50 Y Y N "Name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is ""normal"" if no disease state has been diagnosed." PR_proteomics_sample 16 sample_amount Amount of Sample varchar 50 0 Y N N text 50 Y Y N "Amount of sample initally supplied. Example 1ml, 2kg" PR_proteomics_sample 17 proteomics_sample_protocol_ids Proteomics Sample Protocols varchar 255 0 Y N PR_proteomics_sample_protocol proteomics_sample_protocol_id N multilink 4 Y Y N Select all protocols that apply to this biomaterial. Describe sequence of protocols in the Treatment Description below "SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE P.record_status != 'D' ORDER BY P.name" PR_proteomics_sample 18 protocol_deviations Protocol Deviations text 16 0 Y N N textarea 4 Y Y N Describe any deviations from the selected protocols PR_proteomics_sample 19 sample_description Sample Description text 16 0 Y N N textarea 4 Y Y N Describe the biomaterial briefly PR_proteomics_sample 20 sample_preparation_date Sample Preparation Date datetime 8 0 Y N N text 30 Y Y Y Date/time the biomaterial was prepared with the described protocols PR_proteomics_sample 21 treatment_description Treatment Description text 16 0 Y N N textarea 4 Y Y N "Describe the treatment of the biomaterials, including mention of the selected protocols" PR_proteomics_sample 22 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional notes PR_proteomics_sample 23 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N Y N PR_proteomics_sample 24 created_by_id Record Created By int 4 0 N N contact contact_id N N Y PR_proteomics_sample 25 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N N PR_proteomics_sample 26 modified_by_id Record Modified By int 4 0 N N contact contact_id N N Y PR_proteomics_sample 27 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N Y PR_proteomics_sample 28 record_status Record Status char 1 0 N N N N N N PR_proteomics_sample_protocol 1 proteomics_sample_protocol_id Proteomics Sample Protocol ID int 4 0 N Y Y N N N pkDEFAULT PR_proteomics_sample_protocol 2 proteomics_sample_id Proteomics Sample ID int 4 0 N N PR_proteomics_sample proteomics_sample_id Y Y N Y PR_proteomics_sample_protocol 3 protocol_id Protocol ID int 4 0 N N protocol protocol_id Y N N Y Protocol ID PR_proteomics_sample_protocol 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_sample_protocol 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_proteomics_sample_protocol 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_proteomics_sample_protocol 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_proteomics_sample_protocol 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_proteomics_sample_protocol 9 record_status Record Status char 1 0 N N N N N PR_experiments_samples 1 experiments_samples_id Experiments Samples ID int 4 0 N Y Y N N Y Linking table for experiments and proteomic samples pkDEFAULT PR_experiments_samples 2 experiment_id Proteomic Experiment Name int 4 0 N N PR_proteomics_experiment experiment_id Y optionlist Y Y Y Proteomics Experiment Name tag MANUAL PR_experiments_samples 3 proteomics_sample_id Proteomics Sample Name int 4 0 N N PR_proteomics_sample proteomics_sample_id Y optionlist Y Y Y Proteomics Sample Name tag MANUAL PR_experiments_samples 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N PR_experiments_samples 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N PR_experiments_samples 6 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N PR_experiments_samples 7 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N PR_experiments_samples 8 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N PR_experiments_samples 9 record_status Record Status char 1 0 N N N N N APD_peptide_summary 1 peptide_summary_id Peptide Summary ID int 4 0 N Y N N pkDEFAULT APD_peptide_summary 2 project_id Project int 4 0 N N project project_id Y optionlist Y Y N Project to which the peptide summary belongs "SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id" APD_peptide_summary 3 peptide_summary_name Peptide Summary Title varchar 100 0 N N Y text 50 Y Y Y Title of this peptide summary APD_peptide_summary 4 description Peptide Summary Description text 16 0 N N Y textarea 4 Y Y N "Description of this APD peptide summary, from where it is derived, etc." APD_peptide_summary 5 minimum_probability Minimum Probability real 4 0 N N Y text 10 Y Y N Minimum P value for selecting good peptides APD_peptide_summary 6 experiment_list Search Batch ID List varchar 512 0 N N Y text 50 Y Y N List of search batch ids APD_peptide_summary 7 n_experiments Number of Experiments int 4 0 N N Y text 10 Y Y N Total number of experiments used for this summary APD_peptide_summary 8 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments APD_peptide_summary 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N APD_peptide_summary 10 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N APD_peptide_summary 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N APD_peptide_summary 12 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N APD_peptide_summary 13 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N APD_peptide_summary 14 record_status Record Status char 1 0 N N N N N APD_aggregated_peptide 1 peptide_id APD Peptide ID int 4 0 N Y Y N APD_aggregated_peptide 2 peptide_summary_id APD Peptide Summary ID int 4 0 N N APD_peptide_summary peptide_summary_id Y APD_aggregated_peptide 3 peptide_identifier_id APD Peptide Identifier ID int 4 0 N N APD_peptide_identifier peptide_identifier_id Y APD_aggregated_peptide 4 biosequence_id BioSequence ID int 4 0 N N PR_biosequence biosequence_id N APD_aggregated_peptide 5 biosequence_name BioSequence Name varchar 255 0 N N N APD_aggregated_peptide 6 peptide Peptide varchar 512 0 N N N APD_aggregated_peptide 7 n_peptides Number of Peptides int 4 0 N N N APD_aggregated_peptide 8 experiment_list Search Batch ID List varchar 255 0 N N N APD_aggregated_peptide 9 n_experiments Number of Experiments int 4 0 N N N APD_aggregated_peptide 10 maximum_probability Maximum Probability real 4 0 N N N APD_peptide_summary_experiment 1 peptide_summary_id APD Peptide Summary ID int 4 0 N N APD_peptide_summary peptide_summary_id Y APD_peptide_summary_experiment 2 proteomics_experiment_id Proteomics Experiment ID int 4 0 N N PR_proteomics_experiment experiment_id Y APD_peptide_identifier 1 peptide_identifier_id APD Peptide Identifier ID int 4 0 N Y N APD_peptide_identifier 2 peptide_identifier_str APD Peptide Identifier (f. ex. PAp12345678) varchar 50 0 N N Y APD_peptide_identifier 3 peptide APD Peptide aa sequence varchar 512 0 N N N APD_modified_peptide 1 modified_peptide_id Modified Peptide ID int 4 0 N Y N APD_modified_peptide 2 peptide_id APD Peptide ID int 4 0 N N APD_aggregated_peptide peptide_id Y APD_modified_peptide 3 peptide_string APD Peptide String varchar 512 0 N N Y APD_modified_peptide 4 charge_state Charge State int 4 0 N N N APD_modified_peptide 5 n_modified_peptides Number of Modified Peptides int 4 0 N N N APD_modified_peptide 6 experiment_list Experiment List varchar 255 0 N N N APD_modified_peptide 7 n_experiments Number of Experiments int 4 0 N N N APD_modified_peptide 8 maximum_probability Maximum Probability real 4 0 N N N APD_modified_peptide 9 calc_peptide_mass Calculated Peptide Mass real 4 0 N N N APD_modified_peptide 10 precursor_mass_avg Avg of Precursor Ion Mass real 4 0 N N N APD_modified_peptide 11 precursor_mass_stdev SD of Precorsor Ion Mass real 4 0 Y N N APD_modified_peptide 12 percent_ACN_avg Avg of Percent Acetonitrile real 4 0 Y N N APD_modified_peptide 13 percent_ACN_stdev SD of Percent Acetonitrile real 4 0 Y N N APD_modified_peptide 14 pI_avg Avg pI real 4 0 Y N N APD_modified_peptide 15 SCX_avg Avg SCX Value real 4 0 Y N N APD_peptide_property_type 1 peptide_property_type_id Peptide Property Type ID int 4 0 N Y N APD_peptide_property_type 2 peptide_property_type_name Peptide Property Type Name varchar 100 0 N N Y APD_peptide_property_type 3 peptipe_property_type_decription Peptide Property Type Description text 16 0 Y N N APD_peptide_property_type 4 comment Comment text 16 0 Y N N APD_peptide_property_type 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N APD_peptide_property_type 6 created_by_id Record Created By int 4 0 N N contact contact_id N APD_peptide_property_type 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N APD_peptide_property_type 8 modified_by_id Record Modified By int 4 0 N N contact contact_id N APD_peptide_property_type 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N APD_peptide_property_type 10 record_status Record Status char 1 0 N N N N APD_modified_peptide_property 1 modified_peptide_property_id Modified Peptide Property ID int 4 0 N Y N APD_modified_peptide_property 2 modified_peptide_id Modified Peptide ID int 4 0 N N APD_modified_peptide modified_peptide_id Y APD_modified_peptide_property 3 peptide_property_type_id Peptide Property Type ID int 4 0 N N APD_peptide_property_type peptide_property_type_id Y APD_modified_peptide_property 4 min_value Minimum Value real 4 0 N N N APD_modified_peptide_property 5 max_value Maximum Value real 4 0 N N N APD_modified_peptide_property 6 average_value Avg Value real 4 0 N N N APD_modified_peptide_property 7 standard_deviation SD real 4 0 Y N N APD_modified_peptide_property 8 median_value Mean real 4 0 Y N N APD_modified_peptide_property 9 SIQR SIQR real 4 0 Y N N APD_modified_peptide_property 10 N_values Number of Values int 4 0 N N N APD_BrowseAPD 1 peptide_summary_id APD Summary ID N multioptionlist 4 Y Y N Select the desired APD peptide summaries to search. It is best to select just one. "SELECT peptide_summary_id,peptide_summary_name FROM $TBAPD_PEPTIDE_SUMMARY WHERE record_status != 'D' ORDER BY peptide_summary_name" APD_BrowseAPD 2 probability_constraint Probability Constraint N text 20 Y Y N "Constraint for the maximum probability of the peptide. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" APD_BrowseAPD 3 APD_accession_constraint APD Accession Number N text 20 Y Y N Constraint for the APD peptide accession number (e.g. PAp00002334). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 4 charge_constraint Charge Constraint N optionlist Y 1 N "Constraint for the charge states to include in the query. If blank, all states are included" "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value" APD_BrowseAPD 5 reference_constraint Protein Name Constraint N text 40 Y 1 N Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 6 description_constraint Reference Description Constraint N text 40 Y 2 N Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 7 gene_name_constraint Gene Name Constraint N text 40 Y 2 N Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 8 molecular_function_constraint Molecular Function Constraint N text 40 Y 2 N Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 9 biological_process_constraint Biological Process Constraint N text 40 Y 2 N Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 10 cellular_component_constraint Cellular Component Constraint N text 40 Y 2 N Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 11 protein_domain_constraint Protein Domain Constraint N text 40 Y 2 N Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 12 fav_codon_frequency_constraint Favored Codon Frequency Constraint N text 40 Y 2 N "Constraint for the favored codon frequency (calculation by Patrick Pedrioli). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" APD_BrowseAPD 13 transmembrane_class_constraint Transmembrane Class Constraint N multioptionlist 3 Y 2 N Constraint for the transmembrane class as annotated by TMHMM and SignalP "SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class" APD_BrowseAPD 14 n_transmembrane_regions_constraint Number of Transmembrane Regions Constraint N text 40 Y 2 N "Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau). Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" APD_BrowseAPD 15 accession_constraint Accesssion Number N text 40 Y 2 N Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 16 peptide_constraint Peptide N text 40 Y 2 N Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 17 peptide_string_constraint Peptide String Constraint N text 40 Y 2 N Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported. APD_BrowseAPD 18 peptide_options Peptide Options N multioptionlist 3 Y 1 N Various selectable options to further contrain the peptides displayed "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value" APD_BrowseAPD 19 precursor_mass_constraint Precursor Mass constraint N text 40 Y 1 N "Constraint for the measured precursor mass (as a single decimal value). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" APD_BrowseAPD 20 percent_buffer_b_constraint % Buffer B (ACN) constraint N text 40 Y 2 N "Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" APD_BrowseAPD 21 isoelectric_point_constraint pI constraint N text 40 Y 2 N "Constraint for the theoretical isoelectric point (pI). Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n""" APD_BrowseAPD 22 sort_order Sort Order N optionlist Y Y N Desired display sorting order (DESC means descending: highest to lowest) "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAPD_sort_options' ORDER BY sort_order,option_value" APD_BrowseAPD 23 gene_annotation_level_constraint Gene Annotation Level Constraint N optionlist Y 2 N "Constraint for the hierarchy level of gene annotations to view. By default, the leaf level annotations are displayed" "SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id" APD_BrowseAPD 24 display_options Display Options N multioptionlist 5 Y Y N Various selectable table display options "SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAPD_display_options' ORDER BY sort_order,option_value" APD_BrowseAPD 25 row_limit Maximum Rows N text 10 Y 2 N "Limit the numbers of rows displayed. If not provided, default is 5000 rows."