To specify which columns to display for peptide results:

  • Navigate to the run you would like to work with (see Viewing an MS2 Run).
  • In the Peptides section, select Grid Views > Customize Grid.
  • In the Available Fields pane, select which columns to display in the current view.
  • Click Save to save the grid, either as the default, or as a separate named grid.

Available Peptide Columns

The following table describes some of the available peptide columns which are applicable to all search engines.

Peptide ColumnColumn AbbrevDescription

Scan

 

The number of the machine scan from the run.

RetentionTime

RetTimeThe peptide's elution time.
Run A unique integer identifying the run.
RunDescription A description of the run, including the pep.xml file name and the search protocol name

Fraction

 

The id for a particular fraction, as assigned by the MS2 Viewer. Note that a single run can be comprised of multiple fractions (e.g., if a sample was fractionated to reduce its complexity, and the fractions were interrogated separately on the MS machine, a technician can combine the results for those fractions in a single run file for analysis and upload to the MS2 Viewer).

FractionName The name specified for a given fraction.

Charge

Z

The assumed charge state of the peptide featured in the scan.

IonPercent

Ion%

The number of theoretical fragment ions that matched fragments in the experimental spectrum divided by the total number of theoretical fragment ions, multiplied by 100; higher value indicates a better match.

Mass

CalcMH+

The singly protonated mass of the peptide sequence in the database that was the best match.

DeltaMass

dMass

The difference between the MH+ observed mass and the MH+ theoretical mass of this peptide; a lower number indicates a better match.

DeltaMassPPM

dMassPPM

The difference between the theoretical m/z and the observed m/z , scaled by theoretical m/z and expressed in parts per million; this value gives a measure of the mass accuracy of the MS machine.

FractionalDeltaMassfdMassThe LTQ-FT mass spectrometer may register the C13 peak in error in place of the monoisotopic peak. The FractionalDeltaMass indicates the absolute distance to nearest integer of the DeltaMass, thereby correcting for these errors.
FractionalDeltaMassPPMfdMassPPMThe FractionalDeltaMass expressed in parts per million.

PrecursorMass

ObsMH+

The observed mass of the precursor ion, expressed as singly protonated (MH+).

MZ

ObsMZ

The mass-to-charge ratio of the peptide.

PeptideProphetPepProphetThe score assigned by PeptideProphet. This score represents the probability that the peptide identification is correct. A higher score indicates a better match.
PeptideProphetErrorRatePPErrorRateThe error rate associated with the PeptideProphet probability for the peptide. A lower number indicates a better match.

Peptide

 

The sequence of the peptide match.  The previous and next amino acids in the database sequence are printed before/after the identified peptide, separated by periods.

StrippedPeptide

 

The peptide sequence (including the previous amino acid and next amino acid, if applicable) filtered of all extra characters (no dot at the beginning or end, and no variable modification characters).

PrevAA

 

The amino acid immediately preceding the peptide in the protein sequence; peptides at the beginning of the protein sequence will have a dash (-) as this value.

TrimmedPeptide

 

The peptide sequence without the previous and next amino acids.

NextAA

 

The amino acid immediately following the peptide in the protein sequence; peptides at the end of the protein sequence will have a dash (-) as this value.

ProteinHits

SeqHits

The number of protein sequences in the protein database that contain the matched peptide sequence.

SequencePosition

SeqPos

The position in the protein sequence where the peptide begins.

H

 

Theoretical hydrophobicity of the peptide calculated using Krokhin’s algorithm (Anal. Chem. 2006, 78, 6265).

DeltaScan

dScan

The difference between actual and expected scan number, in standard deviations, based on theoretical hydrophobicity calculation.

Protein

 

A short name for the protein sequence identified by the search engine as a possible source for the identified peptide.

Description

 

A short phrase describing the protein sequence identified by the search engine. This name is derived from the UniProt XML or FASTA file from which the sequence was taken).

GeneName

 

The name of the gene that encodes for this protein sequence.

SeqId A unique integer identifying the protein sequence.

Peptide Columns Populated by ProteinProphet

The following table describes the peptide columns that are populated by ProteinProphet.

Peptide ColumnColumn AbbrevDescription
NSPAdjustedProbabilityNSPAdjProbPeptideProphet probability adjusted for number of sibling peptides.
Weight Share of peptide contributing to the protein identification.
NonDegenerateEvidenceNonDegenEvidTrue/false value indicating whether peptide is unique to protein (true) or shared (false).
EnzymaticTermini Number of expected cleavage termini (valid 0, 1 or 2) consistent with digestion enzyme.
SiblingPeptidesSiblingPepsA calculation, based on peptide probabilities, to quantify sibling peptides (other peptides identified for this protein).
SiblingPeptidesBinSiblingPepsBinA bin or histogram value used by ProteinProphet.
Instances Number of instances the peptide was identified.
ContributingEvidenceContribEvidTrue/false value indicating whether the peptide is contributing evidence to the protein identification.
CalcNeutralPepMass Calculated neutral mass of peptide.

Peptide Columns Populated by Quantitation Analysis

The following table describes the peptide columns that are populated during the quantitation analysis.

Peptide ColumnDescription
LightFirstScanScan number of the start of the elution peak for the light-labeled precursor ion.
LightLastScanScan number of the end of the elution peak for the light-labeled precursor ion
LightMassPrecursor ion m/z of the isotopically light-labeled peptide.
HeavyFirstScanScan number of the start of the elution peak for the heavy-labeled precursor ion.
HeavyLastScanScan number of the end of the elution peak for the heavy-labeled precursor ion.
HeavyMassPrecursor ion m/z of the isotopically heavy-labeled peptide.
RatioLight-to-heavy ratio, based on elution peak areas.
Heavy2LightRatioHeavy-to-light ratio, based on elution peak areas.
LightAreaLight elution peak area.
HeavyAreaHeavy elution peak area.
DecimalRatioLight-to-heavy ratio expressed as a decimal value.

Peptide Columns Specific to X! Tandem

The following table describes the peptide columns that are specific to results generated by the X! Tandem search engine.

Peptide ColumnDescription
HyperTandem’s hypergeometric score representing the quality of the match of the identified peptide; a higher score indicates a better match.
BTandem’s b-ion score.
NextThe hyperscore of the 2nd best scoring peptide.
YTandem’s y-ion score.
ExpectExpectation value of the peptide hit.  This number represents how many identifications are expected by chance to have this hyperscore. The lower the value, the more likely it is that the match is not random.

Peptide Columns Specific to Mascot

The following table shows the scoring columns that are specific to Mascot:

Peptide ColumnDescription

Ion

Mascot ions score representing the quality of the match of the identified peptide; a higher score indicates a better match.

Identity

Identity threshold. An absolute threshold determines from the distribution of random scores to highlight the presence of non-random match. When ions score exceeds identity threshold, there is a 5% chance that the match is not exact.

Homology

Homology threshold. A lower, relative threshold determines from the distribution of random scores to highlight the presence of non-random outliners. When ions score exceeds homology threshold, the match is not random, spectrum may not fully define sequence and the sequence may be close but not exact.

Expect

Expectation value of the peptide hit. This number represents how many identifications are expected by chance to have this ion score or higher. The lower the value, the more likely it is that the match is significant.

Peptide Columns Specific to SEQUEST

The following table shows the scoring columns that are specific to SEQUEST:

Peptide ColumnDescription
SpRankRank of the preliminary SpScore, typically ranging from 1 to 500. A value of 1 means the peptide received the highest preliminary SpScore so lower rankings are better.
SpScoreThe raw value of the preliminary score of the SEQUEST algorithm. The score is based on the number of predicted CID fragments ions that match actual ions and on the predicted presence of immonium ions. An SpScore is calculated for all peptides in the sequence database that match the weight  (+/- a tolerance) of the precursor ion. Typicaly only the top 500 SpScoress are assigned a SpRank and are passed onto the cross correlation analysis for XCorr scoring.
XCorrThe cross correlation score from SEQUEST is the main score that is used to rank the final output. Only the top N (where N normally equals 500) peptides that survive the preliminary SpScoring step undergo cross correlation analysis. The score is based on the cross correlation analysis of a Fourier transform pair ceated from a simulated spectrum vs. the actual spectrum. The higher the number, the better.
DeltaCnThe difference of the normalized cross correlation scores of the top hit and the second best hit (e.g., XC1 - XC2, where XC1 is the XCorr of the top peptide and XC2 is the XCorr of the second peptide on the output list). In general a difference greater than 0.1 indicates a successful match between sequesce and spectrum.

Peptide Columns Specific to COMET

The following table shows the scoring columns that are specific to COMET:

Peptide ColumnDescription

RawScore

Number between 0 and 1000 representing the quality of the match of the peptide feature in the scan to the top COMET database search result; higher score indicates a better match.

ZScore

The number of standard deviations between the best peptide match's score and the mean of the top 100 peptide scores, calculated using the raw dot-product scores; higher score indicates a better match.

DiffScore

The difference between the normalized (normalized from 0.0 to 1.0) RawScore values of the best peptide match and the second best peptide match; greater DiffScore tends to indicate a better match.

Discussion

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