The following table describes the columns on the MS/MS Spectrum Info page.

MS/MS Spectrum Info page columns

Column

Description

# PSMs

Displays the total number of PSMs found for that peptide sequence.

Activation Type

Displays the fragmentation method used to produce the product spectrum.

Best PSM Ambiguity

Displays the “best” ambiguities of the PSMs attached to a spectrum.

This column can display the following categories:

  • Unambiguous: Indicates that this PSM is the only match that the application considered for this spectrum. There is no ambiguity that it needs to resolve.
  • Selected: Indicates that the application selected this PSM from a set of two or more matches that it considered for the protein group inference process.
  • Rejected: Indicates that the application rejected this PSM from a set of two or more matches that it considered for the protein group inference process.
  • Ambiguous: Indicates that the application considered two or more peptide matches to the same spectrum for the protein group inference process. If you set the Apply Strict Parsimony Principle parameter of the Protein Grouping (Enabled) node to True, the application resolves this ambiguity to Selected or to Rejected.
  • Unconsidered: Indicates that the application did not consider this PSM for the protein group inference process because it did not meet the requirements specified by settings of the Protein Grouping node.

For more information on the protein group inference process that the application uses to assign the grouping status of PSMs, see Understanding protein grouping.

Checked

Indicates whether the item is selected.

Creator Node No

Displays the number of the node in the workflow that created the spectrum.

File ID

Displays a short identifier of the input file that the spectrum belongs to.

First Scan

Displays the number of the first scan in grouped scans used to produce the composite search input scan, if scans are grouped.

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 MS/MS Spectrum page displays the Ion Inject Time [ms] column by default for every searched spectrum and every PSM for newly processed data.

Isolation Interference [%]

Displays the percentage of interference by coisolation within the precursor isolation window. The application calculates the isolation interference only for precursors from MS1 spectra with high resolution. For more information on coisolation, see Excluding PSMs with high levels of coisolation.

Last Scan

Displays the number of the last scan in grouped scans used to produce the composite search input scan, if scans are grouped.

The last scan might not be the same as the first scan if the workflow enabled grouped scans.

Mass Analyzer

Displays the mass analyzer used to create the raw data file. The application recognizes the following mass analyzers:

  • ITMS (Ion Trap)
  • FTMS (Fourier Transform)
  • TOFMS (Time of Flight)
  • SQMS (Single Quad)
  • TQMS (Triple Quad)
  • SectorMS (Sector Field)

Master Scan(s)

Displays the master scans of the scans that the application used to derive the actual scan, usually one MS1 scan.

MS Order

Indicates the order of the MS spectrum:

  • MS1 is one MS scan.
  • MS2 is an MS/MS scan.
  • MS3 is an MS3 scan.

Original Mass

Displays the original mass of the precursor ion.

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 the Xtract algorithm.

Precursor Charge

Displays the charge state of the precursor ion.

Precursor Intensity

Displays the intensity of the precursor ion.

Precursor m/z [Da]

Displays the mass-to-charge ratio of the precursor ion, in daltons.

Precursor MH+ [Da]

Displays the singly charged mass of the precursor ions, in daltons.

RT [min]

Displays the retention time when the application observed the peptide, in minutes.

Scan(s)

Displays the scans from which the actual scan was derived. Usually it is a single scan, but a grouping node might group several scans together.

SearchID

Displays the order in which the search was submitted to the job queue.

Spectrum File

Displays the name of the file containing the spectra.