The following table describes the columns on the PSMs page.
Column | Description |
|---|---|
# Missed Cleavages | Displays the number of cleavage sites in a peptide sequence that a cleavage reagent (enzyme) did not cleave. This number excludes cases where an amino acid, such as proline, inhibits the cleaving enzyme. For example, if proline resides next to lysine or arginine, trypsin does not cleave the lysine or arginine. The application returns a 0 value for the # Missed Cleavages when all peptides have been completely digested. |
# Protein Groups | Displays the number of protein groups that include the peptide. |
# Proteins | Displays the number of proteins that include the PSM. |
Abundances | Displays the abundances of the quantification channels. |
Activation Type | Displays the activation type of the spectrum where the application identified the peptide. |
Annotated Sequence | Displays the names of the flanking residues of a peptide in a protein. |
Average Reporter S/N | Displays the average reporter S/N values, which the application calculates as the sum of S/N values found divided by the number of defined tags. You can set a threshold that determines which items appear in this column by using the Average Reporter S/N Threshold parameter of the Reporter Ions Quantifier node. |
Charge | Displays the charge state of the peptide. |
Checked | Indicates whether the item is selected. |
Concatenated Rank | Displays the value for the best PSM that the search engine found. This value includes the rank of the decoy PSMs for the same spectra. |
Confidence | Indicates a confidence level associated with the peptide sequence at the top level:
|
File ID | Displays the short identifier of the input file that the fragment spectrum belongs to. |
First Scan | Displays the number of the first scan used to identify the peptide. |
Identified by Inclusion File | Displays the PSMs identified at lower confidence by an optimized search using match information from the CHIMERYS inclusion file. |
Identifying Node | Displays the name of the search engine node, the letter representing the number of MSF files used to generate the result file, and the number assigned to the node in the workflow. |
Identifying Node No | Displays the number assigned to the node in the workflow. |
Identifying Node Type | Displays the name of the search engine node. |
Intensity | Displays the intensity of the precursor ion. |
Ion Inject Time [ms] | Specifies the time, in milliseconds, used to accumulate ions in the mass spectrometer to reach their target value before they are scanned out. Low ion injection times are desirable because they indicate high transmission and fast cycle times. Ion injection times that slowly increase might indicate lower transmission, the need for multiplier gain calibration, or both. The PSMs page displays the Ion Inject Time [ms] column by default for every searched spectrum and every PSM for newly processed data. |
Ions Matched | Displays the ratio. |
Isolation Interference [%] | Displays the percentage of interference by co-isolation within the precursor isolation window. The application does not populate this column for a PQD quantification report. It calculates the isolation interference only for precursors from MS1 spectra with high resolution. For more information on co-isolation, see Excluding PSMs with high levels of coisolation. |
Last Scan | Displays the number of the last scan used to identify the peptide. The last scan might not be the same as the first scan if the workflow enabled grouped scans. |
m/z [Da] | Displays the mass-to-charge ratio of the precursor ion, in daltons. |
Master Protein Accessions | Displays the unique identifiers (accessions) of all master proteins from all protein groups that include the given peptide sequence. This column appears when you use the Protein Grouping node in the consensus workflow. |
Master Protein Descriptions | Displays a description of the master proteins. |
Master Scan(s) | Displays the precursor scan number or numbers. |
Matched Ions | Displays the number of ions matched by the search engine. |
MH+ [Da] | Displays the protonated monoisotopic mass of the peptides, in daltons. It is the measured mass, as opposed to the expected mass in the Theo. MH+ [Da] column. |
Modifications | Displays the static and dynamic modifications identified in the peptide. |
MS Order | Indicates the order of the MS spectrum as follows:
|
Original Precursor Charge | Displays the charge state of the precursor as stored in the scan header of the raw data file. This value is different from the actual charge state if you use charge deconvolution, for example, by using Xtract. |
Peptides Matched | Displays the number of peptide candidates that fall into the precursor mass tolerance window set for the search. |
Percolator PEP | Displays the posterior error probability (PEP) for the identified peptide. This column appears when the processing workflow includes the Percolator node. For information on how this node calculates the posterior error probability, see Posterior Error Probability (PEP). |
Percolator q-Value | Displays the q-value of the best PSM if the peptide groups that the search node identified. This column appears when the consensus workflow includes the Percolator node. For information on how this node calculates the q-value, see q-value. |
Percolator SVMScore | Displays the maximum Percolator score for the identified peptide. This column appears when the processing workflow includes the Percolator node. For information on this node, see Percolator node. |
Protein Accessions | Displays the unique identifiers (accessions) of all proteins that include the given peptide sequence. The identifiers displayed in the Protein Group Accessions column are the same as those displayed in the Accession column on the Proteins and PSMs pages. |
Protein Descriptions | Describes the proteins associated with the peptide. This description is taken from the FASTA file. |
PSM Ambiguity | Displays the grouping status of the PSM. This column can display the following categories:
For more information on the protein group inference process that the application uses to assign the grouping status of PSMs, see Understanding protein grouping. |
Quan Info (in result files with quantification results only) | Indicates why the application used or did not use a peptide in quantification: (For reporter ion quantification)
(For precursor ion quantification)
|
Rank | Displays the ordering of peptides by rank. |
RT [min] | Displays the retention time when the peptide was observed, in minutes. |
Search Engine Rank | Displays the original rank assigned by the search engine. |
Search ID | Displays the order that the application submitted the search to the job queue. |
Sequence | Displays the sequence of amino acids that compose a peptide. Modified amino acids are shown in lowercase letters. In the Unmodified Sequence column, the sequence is displayed in capital letters. |
Spectral Angle | The correlation between the theoretical and experimental spectra calculated by the INFERYS Rescoring node. For more information, see INFERYS Rescoring node. |
Spectrum File | Displays the name of the file containing the spectra. |
Theo. MH+ [Da] | Displays the MH+ mass, in daltons, calculated from the amino acid sequence, including the modifications. It is the expected mass, as opposed to the measured mass in the MH+ [Da] column. |
Total Ions | Displays the total possible number of ions. |
XCorr (Sequest HT searches only) | Scores the number of fragment ions that are common to two different peptides with the same precursor mass and calculates the cross-correlation score for all candidate peptides queried from the database. |
ΔCn | Displays the normalized score difference between the currently selected PSM and the highest-scoring PSM for that spectrum. |
ΔM [ppm] | Displays the difference between the theoretical mass of the peptide and the experimental mass of the precursor ion. |
Δm/z [Da] | Displays the difference between the measured charged mass (m/z [Da]) and the theoretical mass of the same charge (z). |
ΔScore | Displays a measure of the difference between the top two scores for the peptides identified by that spectrum. The application calculates this score as follows. For information about the D score calculation, see The Delta Score column. |
Contaminant | Displays an X symbol next to the proteins marked as contaminants in the searched FASTA file or files. This column appears when the consensus workflow includes the Protein Marker node. For more information, see Protein Marker node. |
Peptide Quan Usage | Shows which PSM abundances are used for peptide quantification. The values are:
The node always uses quantification results of unique peptides for their associated proteins, but it uses quantification results of peptides that are not unique only when razor peptides or all peptides are used. When it uses all peptides, it uses peptides that are not unique for all associated proteins. When the node uses razor peptides, it uses peptides that are not unique for a single protein or those that are only unique for the proteins of a single protein group. |
Annotation | Provides a location for you to insert and store notes about the search results, your analysis, and quality results. |
q-value | Displays the q-value for the identified peptide. This column appears when the processing workflow includes the Percolator node. For information on how this node calculates the q-value, see q-value. |
Ratio columns | Display the corrected ratio of the intensity of the fragmented tag in a sample to the intensity of the fragmented tag in the control sample. |
Flanking Residues | Displays the flanking residues for a PSM. The number of flanking residues displayed is specified in the Peptide in Protein Annotation node. The flanking residues appear in the Annotated Sequence column of a PSM’s associated table (the table that appears when you select a PSM and then select Show Associated Tables). This information appears when you use the Peptide in Protein Annotation node in the consensus workflow. |
Positions in Master Proteins | Displays the position of the peptide within the master protein sequence. This column appears only in a PSM’s associated table (the table that appears when you select a PSM and then select Show Associated Tables). This column appears when you use the Peptide in Protein Annotation node in the consensus workflow. |
SpScore (Sequest HT searches only) | Displays the raw value of the preliminary score of the Sequest HT algorithm. |
Probability (Sequest HT searches only) | Displays the probability score for the peptide. |
MSPepSearch Score (MSPepSearch searches only) | Displays the MSPepSearch score. |
Dot Score (MSPepSearch searches only) | Displays the dot score. |
Rev-Dot Score (MSPepSearch searches only) | Displays the reverse dot score. |
Expectation Value or Exp Value (Mascot searches only) | Displays the expectation value, which is a measure of the number of matches with scores equal to or better than the score values that are expected to occur only by chance. For Mascot, the smaller the expectation value is, the better the match is considered. |
QuanResultID (in result files with quantification results only) | Uniquely identifies a certain quantification result consisting of the quantification values for different quantification channels. For example, if you identify a peptide in both its light and heavy forms, the light and heavy peptides share the same quantification result, so the same identifier appears for both of them in the QuanResultID column. |
# Missing Channels (in result files with isotopically labeled and area calculation quantification results only) | Displays the number of missing channels in the peptide.
|
# Single-Peak Channels (in result files with for isotopically labeled and area calculation quantification results only) | Displays the number of single-peak channels in the peptide.
|
Area (in result files with isotopically labeled and area calculation quantification results only) | Displays the area of the peak for the isotopic cluster for the peptide.
|
Homology Threshold (Mascot searches only) | Sets a threshold that determines whether the proposed peptide sequence and the real sequence are considered similar. Peptides with a score higher than this threshold are at least considered similar or homologous. |
Ions Score (Mascot searches only) | Refer to the Mascot documentation from Matrix Science. |
Identity High (Mascot searches only) | Sets a threshold that determines whether peptides are ranked as high confidence when you perform a decoy search to calculate false discovery rates (FDRs). Peptides with an Ions Score value above this threshold are ranked as high confidence and marked green. |
Identity Middle (Mascot searches only) | Sets a threshold that determines whether peptides are ranked as medium confidence when you perform a decoy search to calculate FDRs. Peptides with an Ions Score value above this threshold are ranked as medium confidence and marked yellow. |
Identity Relaxed (Mascot searches only) | Displays the identity threshold for PSMs of medium confidence. |
Identity Strict (Mascot searches only) | Displays the identity threshold for PSMs of high confidence. |
Quan Channel (in result files with isotopically labeled quantification results only) | Displays the channel name of the peptide that is used for quantification. |
Heavy/Light (in result files with precursor ion quantification results only) | Displays the isotopic label type. This column appears only when you have loaded a result file containing the results of isotopically labeled quantification. |
ptmRS Best Site Probabilities | Displays the most likely positions of the modifications and their site score for each PSM. For peptide groups, this column shows the best site probabilities of the first PSM. This column appears only when the processing workflow includes the IMP-ptmRS node. |
ptmRS Modification Site Probabilities | Displays the modification site probabilities for all possible modification positions for a single modification. In the column title, Modification is replaced by the name of the actual modification, for example, Oxidation Site Probabilities. This column appears only when the processing workflow includes the IMP-ptmRS node. |
ptmRS Binomial Peptide Score | Displays a peptide score based on the cumulative binomial probability that the observed match is a random event. The value of the Binomial Peptide score heavily depends on the data scored, but usually, scores above 50 indicate a good PTM identification. This column appears only when the processing workflow includes the IMP-ptmRS node. |
ptmRS Isoform Confidence Probability | Estimates the probability (0.000–1.000) that the respective isoform is correct. This column appears only when the processing workflow includes the IMP-ptmRS node. |
ptmRS Isoform Group Report | Indicates which fragment ions the application used to differentiate between the two top-scoring isoforms. This column appears only when the processing workflow includes the IMP-ptmRS node. |