Table name and column name listing - Proteome Discoverer Software - Table name and column name listing - Proteome Discoverer Software - Proteome Discoverer Software

Proteins

Abundance Ratio Adj P-Value, Abundance Ratio P-Value, Abundance Ratios, Abundance Ratios log2, Abundances, Abundances Counts, Abundances Grouped, Abundances Grouped Count, Abundances Grouped CV, Abundances Normalized, Abundances Scaled, Accession, Biological Process, calc pI, Cellular Component, Checked, Chromosome, Coverage in Percent, Coverage in Percent by Search Engine, Description, Ensembl Gene ID, Entrez Gene ID, Exp q-value, FASTA Title Lines, Found in Sample Groups, Found in Samples, Gene Symbol, GO Accessions, Master, Modifications, Molecular Function, MW in kDa, Number of AAs, Number of Crosslinks, Number of Decoy Proteins, Number of Isoforms, Number of Peptides, Number of Peptides by Search Engine, Number of Protein Annotation Groups, Number of Protein Groups, Number of Protein Pathway Groups, Number of Protein Unique Peptides, Number of PSMs, Number of PSMs by Search Engine, Number of Razor Peptides, Number of Unique Peptides, Pfam IDs, Protein FDR Confidence, Protein Group IDs, Reactome Pathway Accessions, Reactome Pathway Accessions All, Reactome Pathways, Score Sequest HT, Sequence, Sum PEP Score, WikiPathway Accessions, WikiPathways

Protein Groups

Checked, Found in Sample Groups, Found in Samples, Group Description, Number of Isoforms, Number of Proteins, Number of PSMs, Number of Unique Peptides, Protein Group ID

Peptide Groups

Abundance Ratio, Abundance Ratio Adj P-Value, Abundance Ratio log2, Abundance Ratio P-Value, Abundances, Abundances Counts, Abundances Grouped, Abundances Grouped Count, Abundances Grouped CV, Abundances Normalized, Abundances Scaled, Annotated Sequence, Charge by Search Engine, Checked, Concatenated Rank by Search Engine, Confidence, Confidence by Search Engine, Delta Cn by Search Engine, Delta M in ppm by Search Engine, Delta mz in Da by Search Engine, Delta Score by Search Engine, Found in Sample Groups, Found in Samples, Master Protein Accessions, Master Protein Descriptions, Modifications, Modifications all possible sites, Modifications in Master Proteins, Modifications in Master Proteins all Sites, mz in Da by Search Engine, Number of Isoforms, Number of Missed Cleavages, Number of Protein Groups, Number of Proteins, Number of PSMs, Percolator PEP by Search Engine, Percolator q-Value by Search Engine, Percolator SVMScore by Search Engine, Positions in Master Proteins, Protein Accessions, PSM Ambiguity, Quan Info, Qvality PEP, Qvality q-value, Rank by Search Engine, RT in min by Search Engine, Search Engine Rank by Search Engine, Sequence, Sequence Length, SVM_Score, Theo MHplus in Da, Top Apex RT in min, XCorr by Search Engine, Score CHIMERYS Identification (by search engine)

PSMs

Activation Type, Annotated Sequence, Charge, Checked, Concatenated Rank, Confidence, Delta Cn, Delta M in ppm, Delta mz in Da, Delta Score, File ID, First Scan, Identifying Node, Identifying Node No, Identifying Node Type, Intensity, Ion Inject Time in ms, Ions Matched, Isolation Interference in Percent, Last Scan, Master Protein Accessions, Master Protein Descriptions, Master Scans, Matched Ions, MHplus in Da, Modifications, MS Order, mz in Da, Number of Missed Cleavages, Number of Protein Groups, Number of Proteins, Original Precursor Charge, Peptides Matched, Protein Accessions, Protein Descriptions, PSM Ambiguity, PSMs Peptide ID, PSMs Workflow ID, Rank, RT in min, Search Engine Rank, Search ID, Sequence, Spectrum File, Theo MHplus in Da, Total Ions, XCorr, Spectral Angle, CHIMERYS Ion Coefficient, Normalized coefficient, Identified by Inclusion File, Quan value

MS/MS Spectrum Info

Activation Type, Best PSM Ambiguity, Checked, Creator Node No, File ID, First Scan, Ion Inject Time in ms, Isolation Interference in Percent, Last Scan, Mass Analyzer, MS Order, MSMS Spectrum Info Spectrum ID, Number of Master Scans, Number of PSMs, Number of Scans, Original Mass, Original Precursor Charge, Precursor Charge, Precursor Intensity, Precursor MHplus in Da, Precursor mz in Da, RT in min, Scans, Search ID, Spectrum File

Input Files

Creation Date, File ID, File Name, Input Files, Input Files Workflow Level, Instrument Hardware, Instrument Name, Ref File ID, RT Range in min, Software Revision

CSMs

All Scans, Charge, Charges A, Charges B, Checked, Confidence, Crosslink localisation probability, Crosslink Strategy, Crosslink Type, Crosslinker, Crosslinker Position A, Crosslinker Position B, CSMs, Delta XlinkX Score, Delta M in ppm, File ID, First Scan, Gene Name A, Gene Name B, Gene Names, Identified By, Identifying Node No, Is Decoy, Leading Protein Position A, Leading Protein Position B, MHplus in Da, Modifications A, Modifications B, mz in Da, Mzs A in Da, Mzs B in Da, Number of Identified MS2 Scans, Number of Identified MS3 Scans, Protein Descriptions A, Protein Descriptions B, Reporter Ion Score, RT in min, Sequence, Sequence A, Sequence B, Spectrum File, Spectrum file path, XlinkX Score

Crosslink Summary

Crosslink Summary, Number CSM's, Number interlinks, Number intralinks, Number of isotopes re-sequenced MS2, Number of isotopes re-sequenced MS3, Number of isotopes sequenced MS2, Number of isotopes sequenced MS3, Number Reporters, Raw file

Crosslinks

Accession A, Accession B, Ambiguity, Checked, Confidence, Crosslink localization probability, Crosslink Sequence, Crosslink Type, Crosslinker, Crosslinks, Crosslinks Peptide Group ID, Max XlinkX Score, Modifications A, Modifications B, Number of CSMs, Number of Proteins, Position A, Position B, Protein Descriptions A, Protein Descriptions B, PSM Ambiguity, Sequence A, Sequence B

Crosslink Reporter Peaks

Charge, Charge xA, Charge xB, Crosslink event, Crosslink Reporter Peaks, Crosslink Strategy, Crosslinker, Diagnostic Peaks Isotope Error, Diagnostic Peaks p-Value, Fragmentation efficiency, Fragmentation Scan Numbers, Fragmentation Spectrum IDs, Intensity, Mass in Da, Modification definitions A, Modification definitions B, Modifications A, Modifications B, mz in Th, mz xA in Th, mz xB in Th, Pre Scan Number, Pre Spectrum ID, Relative presence, Retention Time in min, Scan Number, Spectrum File Path, Spectrum ID, Unmodified Mass xA in Da, Unmodified Mass xB in Da,

Crosslink MS3 Scans

Crosslink Event, Crosslink localisation probability, Crosslink MS3 Scans, Crosslink Reagent, Crosslink Strategy, Definition of Peptide, Delta M in ppm, First Scan, Fraction, FractionIonsMatchedAseries, FractionIonsMatchedBseries, FractionIonsMatchedCseries, FractionIonsMatchedXseries, FractionIonsMatchedYseries, FractionIonsMatchedZseries, Fragment mz error, Fragment mz error IQR, Fragment mz error IQR ppm, Fragment mz error ppm, Fragmentation efficiency, Gene Names, Identification Delta Score, Identification Score, Identification Usage, IntensityIonsMatchedAseries, IntensityIonsMatchedBseries, IntensityIonsMatchedCseries, IntensityIonsMatchedXseries, IntensityIonsMatchedYseries, IntensityIonsMatchedZseries, Is Decoy, Is Significant, Isolation Interference, Leading Protein, Leading Protein Crosslink Position, Master Scan, Matched Ion Count, Missed Cleavages, Modifications, Number of Matches, Number of Modifiable Residues, Number of Modified Residues, Number of Unique Variable Modifications, Peptide ID, Peptide Position, Precursor Charge, Precursor Isotope Offset, Precursor MHplus in Da, Precursor mz in Th, Protein Crosslink Positions, Protein Descriptions, Reporter ID, Reporter Score, RT in min, Sequence, Sequence Coverage, Spectrum File Path, Theoretical Mass in Da, Total Ion Count, Validator Q-value

Crosslink MS2 Scans

Annotated Sequences, Charge State Peptide A, Charge State Peptide B, Crosslink Event, Crosslink localisation probability A, Crosslink localisation probability B, Crosslink MS2 Scans, Crosslink Positions A, Crosslink Positions B, Crosslink Reagent, Crosslink Strategy, Crosslink Type, Definition of Peptide A, Definition of Peptide B, Delta M A in ppm, Delta M B in ppm, Delta M in ppm, First Scan, Fraction, FractionIonsMatchedAseries, FractionIonsMatchedBseries, FractionIonsMatchedCseries, FractionIonsMatchedXseries, FractionIonsMatchedYseries, FractionIonsMatchedZseries, Fragment mz error, Fragment mz error IQR, Fragment mz error IQR ppm, Fragment mz error ppm, Fragmentation efficiency, Gene Names A, Gene Names B, Identification Delta Score, Identification Score, Identification Usage, IntensityIonsMatchedAseries, IntensityIonsMatchedBseries, IntensityIonsMatchedCseries, IntensityIonsMatchedXseries, IntensityIonsMatchedYseries, IntensityIonsMatchedZseries, Is Decoy, Is Significant, Isolation Interference, Leading Crosslink Position A, Leading Crosslink Position B, Leading Protein A, Leading Protein B, Master Scan, Matched Ion Count, Missed Cleavages A, Missed Cleavages B, Modifications A, Modifications B, mz's Peptide A in Da, mz's Peptide B in Da, Number of Matches A, Number of Matches B, Number of Modifiable Residues A, Number of Modifiable Residues B, Number of Modified Residues A, Number of Modified Residues B, Number of Unique Variable Modifications A, Number of Unique Variable Modifications B, Peptide ID A, Peptide ID B, Peptide Position A, Peptide Position B, Precursor Charge, Precursor Isotope Offset, Precursor MHplus in Da, Precursor mz in Th, Protein Descriptions A, Protein Descriptions B, Reporter ID, Reporter Score, RT in min, Sequence A, Sequence B, Sequence Coverage A, Sequence Coverage B, Spectrum File Path, Theoretical Mass in Da, Total Ion Count, Unmodified mass Peptide A MHplus in Da, Unmodified Mass Peptide B MHplus in Da, Validator Q-value

Crosslink Full Scan Statistics

Crosslink Full Scan Statistics, Cycle time, Number of MS2 scans, Number of MS3 scans, Raw file, Retention time, Scan number

Specialized Traces

Checked, Description, File ID, Scan Filter, Specialized Traces ID, Spectrum File, TraceDetector Type

Result Statistics

Arithmetic Mean, Count, CV, IQR, Maximum, Median, Minimum, Name, Result Statistics ID, SD, Sum

Pathway Protein Groups

Checked, Number of Master Proteins, Number of Proteins, Pathway Accession, Pathway Description, Pathway Level, Pathway Protein Groups Group ID, Pathway Source

Consensus Features

Abundances Count (Distribution), Abundances Normalized (Distribution), Abundances Origin (Distribution), Abundances per File (Distribution), Avg Apex RT in min, Avg mz in Da, Charge, Checked, Consensus Features, Delta ApexRT in min, Delta M in ppm, Left RT in min, Max Apex SN, Number of Isotopes, Number of Peptides, Number of PSMs, Quan Info, Quan Info Details, Right RT in min

Annotation Protein Groups

Annotation Accession, Annotation Description, Annotation Level, Annotation Protein Groups Group ID, Annotation Source, Checked, Number of Master Proteins, Number of Proteins

PrSMs

Activation Type, Annotated Sequence, C Score, Charge, Checked, Confidence, Corrected Delta Mass Da, Corrected Delta Mass ppm, Delta Mass in Da, Delta Mass in ppm, External Top Down Displays, File ID, Fragment Count, Fragmentation Scans, Identifying Node, Identifying Node No, Identifying Node Type, Intensity, Ion Inject Time in ms, Ions Matched in Percent, Ions Matched in Percent, -Log E-Value, -Log P-Score, Mass in Da, Matched Ions, Modifications, MS Order, mz in Da, Number of Fragmentation Scans, Number of Precursor Scans, Number of Proteins, Original Precursor Charge, Percent Residue Cleavages, Precursor Scans, Protein Accessions, Protein Descriptions, PrSMs PrSM ID, PrSMs Workflow ID, Q-Value, Rank, RT in min, Search Engine Rank, Search ID, Sequence, Spectrum File, Theo Mass in Da, Total Ions, XCorr

Modification Sites

Checked, Confidence, Master, Modification Name, Modification Sites Modification Site ID, Modification Sites Workflow ID, Motif, Number of Modified PSMs, Number of Unmodified PSMs, Peptide Sequence, Position, Position in Peptide, Protein Accession, Protein Description, Site Probability, Target Amino Acid

Quan Spectra

Abundance, Abundances Normalized, Activation Type, Average Reporter SN, Best PSM Ambiguity, Checked, Creator Node No, File ID, First Scan, Ion Inject Time in ms, Isolation Interference in Percent, Last Scan, Mass Analyzer, Master Scans, MS Order, Number of Master Scans, Number of PSMs, Number of Scans, Original Mass, Original Precursor Charge, Precursor Charge, Precursor Intensity, Precursor MHplus in Da, Precursor mz in Da, Quan Info, Quan Info Details, Quan Spectra Spectrum ID, Quan Spectra Workflow ID, RT in min, Scans, Search ID, Spectrum File

Peptide Isoforms

Abundance, Abundance Ratio, Abundance Ratio Adj P-Value, Abundance Ratio log2, Abundance Ratio P-Value, Abundances Count, Abundances Grouped, Abundances Grouped Count, Abundances Grouped CV in Percent, Abundances Normalized, Abundances Scaled, Charge by Search Engine, Checked, Concatenated Rank by Search Engine, Confidence by Search Engine, Delta Cn by Search Engine, Delta M in ppm by Search Engine, Delta mz in Da by Search Engine, Delta Score by Search Engine, Master Protein Accessions, Master Protein Descriptions, Modification Pattern, Modifications, mz in Da by Search Engine, Number of Isoforms, Number of Missed Cleavages, Number of Protein Groups, Number of Proteins, Number of PSMs, Peptide Isoforms Peptide Group ID, Percolator PEP by Search Engine, Percolator q-Value by Search Engine, Percolator SVMScore by Search Engine, Protein Accessions, PSM Ambiguity, Quan Info, Rank by Search Engine, RT in min by Search Engine, Search Engine Rank by Search Engine, Sequence, Sequence Length, Theo MHplus in Da, XCorr by Search Engine

Peptide Isoforms

Abundance, Abundance Ratio, Abundance Ratio Adj P-Value, Abundance Ratio log2, Abundance Ratio P-Value, Abundances Count, Abundances Grouped, Abundances Grouped Count, Abundances Grouped CV in Percent, Abundances Normalized, Abundances Scaled, Charge by Search Engine, Checked, Concatenated Rank by Search Engine, Confidence by Search Engine, Delta Cn by Search Engine, Delta M in ppm by Search Engine, Delta mz in Da by Search Engine, Delta Score by Search Engine, Master Protein Accessions, Master Protein Descriptions, Modification Pattern, Modifications, mz in Da by Search Engine, Number of Isoforms, Number of Missed Cleavages, Number of Protein Groups, Number of Proteins, Number of PSMs, Peptide Isoforms Peptide Group ID, Percolator PEP by Search Engine, Percolator q-Value by Search Engine, Percolator SVMScore by Search Engine, Protein Accessions, PSM Ambiguity, Quan Info, Rank by Search Engine, RT in min by Search Engine, Search Engine Rank by Search Engine, Sequence, Sequence Length, Theo MHplus in Da, XCorr by Search Engine

Isoforms

Accession, Biological process, Calc pi, Cellular component, Checked, Description, Ensembl gene id, Entrez gene id, Fasta title lines, Gene symbol, Go accessions, Isoforms unique sequence id, Molecular function, Mw in kda, Number of aas, Number of characterized proteoforms, Number of protein annotation groups, Number of protein pathway groups, Number of proteoforms, Number of prsms, Pfam ids, Proteoform characterization confidence, Q-value, Sequence

Proteoforms (only for ProSightPD)

Average PrSM Detected Neutral Mass, Best PrSM C-Score, Charge by Search Engine ProSightPD Absolute Mass Search, Charge by Search Engine ProSightPD BioMarker Search, Charge by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Charge by Search Engine ProSightPD Gene Restricted BioMarker Search, Checked, Confidence, Confidence by Search Engine ProSightPD Absolute Mass Search, Confidence by Search Engine ProSightPD BioMarker Search, Confidence by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Confidence by Search Engine ProSightPD Gene Restricted BioMarker Search, Delta Mass in Da by Search Engine ProSightPD Absolute Mass Search, Delta Mass in Da by Search Engine ProSightPD BioMarker Search, Delta Mass in Da by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Delta Mass in Da by Search Engine ProSightPD Gene Restricted BioMarker Search, Delta Mass in ppm by Search Engine ProSightPD Absolute Mass Search, Delta Mass in ppm by Search Engine ProSightPD BioMarker Search, Delta Mass in ppm by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Delta Mass in ppm by Search Engine ProSightPD Gene Restricted BioMarker Search, External Top Down Displays, -Log E-Value by Search Engine ProSightPD Absolute Mass Search, -Log E-Value by Search Engine ProSightPD BioMarker Search, -Log E-Value by Search Engine ProSightPD Gene Restricted Absolute Mass Search, -Log E-Value by Search Engine ProSightPD Gene Restricted BioMarker Search, -Log P-Score by Search Engine ProSightPD Gene Restricted Absolute Mass Search, -Log P-Score by Search Engine ProSightPD Gene Restricted BioMarker Search, mz in Da by Search Engine ProSightPD Absolute Mass Search, mz in Da by Search Engine ProSightPD BioMarker Search, mz in Da by Search Engine ProSightPD Gene Restricted Absolute Mass Search, mz in Da by Search Engine ProSightPD Gene Restricted BioMarker Search, Number of Proteins, Number of PrSMs, Percent Residue Cleavages, Protein Accessions, Proteoform Characterization Confidence, Proteoforms Proteoform Group ID, Q-value, Rank by Search Engine ProSightPD Absolute Mass Search, Rank by Search Engine ProSightPD BioMarker Search, Rank by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Rank by Search Engine ProSightPD Gene Restricted BioMarker Search, RT in min by Search Engine ProSightPD Absolute Mass Search, RT in min by Search Engine ProSightPD BioMarker Search, RT in min by Search Engine ProSightPD Gene Restricted Absolute Mass Search, RT in min by Search Engine ProSightPD Gene Restricted BioMarker Search, Search Engine Rank by Search Engine ProSightPD Absolute Mass Search, Search Engine Rank by Search Engine ProSightPD BioMarker Search, Search Engine Rank by Search Engine ProSightPD Gene Restricted Absolute Mass Search, Search Engine Rank by Search Engine ProSightPD Gene Restricted BioMarker Search, Sequence, Sequence Length, Theo Mass in Da

Study Information

Study Information: Sample, File ID, Sample Identifier, File Name, Sample Type, Quan Method, Quan Channel, Sample Group, Ratios

This table also has columns for each study factor that is defined by the user with the prefix. The format is CF, NF, or BF followed by the study factor name.