The CSMs page lists the single identified CSMs and their properties. CSMs provide the key evidence of an identified crosslinker. Depending on the method, the CSM includes the crosslink search results of one, two, five, or six spectra that are acquired from the same MS1 precursor mass. The columns in the CSM table show the mass values, the crosslink reagent, and the sequence of the connected crosslinks, as well as those of single peptides.
The following figure gives an example of the CSMs page. Double-clicking a row in the CSM table opens a new dialog box that shows the annotated spectra that were used to identify the crosslinks.
After the search, you can double-click a CSM to display the fragment match spectra. The fragment spectra open in a separate dialog box, and the display differs, depending on which acquisition strategy you used.
See MS2 Only for MS-Cleavable Linker Method for an example of the number of the identified spectra per acquisition strategy.
Procedure
- To view charts on the CSMs page, do the following:
- Double-click a row on the CSMs page to open the Crosslink Spectrum Match Identification Details chart.
For information about this chart, see Crosslink Spectrum Match Identification Details View.
The following table describes the columns on the CSMs page of the result file.
Column | Description |
|---|---|
Sequence | Displays the sequence of the two crosslinked peptides. |
Charge | Displays the charge of the peptide. |
Checked | Indicates whether the item is selected. |
Crosslink localisation probability | Indicates probability of the crosslink site identification. |
Crosslink Strategy | Displays the acquisition mode. |
Crosslink Type | Indicates how a peptide is crosslinked:
|
Crosslinker | Displays the name of the chemical that binds the two peptides given in the Sequence letter columns. |
Crosslinker Position A | Displays the position of the crosslinker in the first peptide. |
Crosslinker Position B | Displays the position of the crosslinker in the second peptide. |
First Scan | Displays the number of the first scan used to identify the peptide. |
Protein Accession A | Displays the name of the gene or the protein accession in the .fasta file associated with the first peptide in the crosslinker. |
Protein Accession B | Displays the name of the gene or the protein accession in the .fasta file associated with the second peptide in the crosslinker. |
Accessions | Displays both names in the Protein Accession A and Protein Accession B columns. |
# Identified MS2 Scans | Displays the number of MS2 scans that identified the crosslinker peptide. |
# Identified MS3 Scans | Displays the number of MS3 scans that identified the crosslinker peptide. |
Is Decoy | Displays whether the CSM is a target or decoy hit. If true, this is a decoy hit; if false, this is a forward database match. |
Leading Protein Position A | Displays the position of the crosslinker of the first crosslinker peptide in the leading protein (=master protein). |
Leading Protein Position B | Displays the position of the crosslinker of the second crosslinker peptide in the leading protein (=master protein). |
M/z [Da] | Displays the mass-to-charge ratio of both crosslinker peptides. |
MH+ [Da] | Displays the mass of both crosslinker peptides. |
Protein Descriptions A | Describes the proteins associated with the first crosslinker peptide. This description is taken from the .fasta file. |
Protein Descriptions B | Describes the proteins associated with the second crosslinker peptide. This description is taken from the .fasta file. |
Reporter Ion Score | Displays the score for reporter ions identified in the MS2 spectrum for MS cleavable crosslinkers. |
RT | Displays the retention time of the crosslinker peptides. |
Δ XlinkX Score | Displays the difference in score between the top and second best hits. |
Sequence A | Displays the sequence of the first crosslinker peptide. |
Sequence B | Displays the sequence of the second crosslinker peptide. |
Spectrum File Path | Displays the name and path of the raw data file. |
XlinkX Score1) | Displays a score that reflects the number of matching fragments relative to the total number of potential fragments for the target peptide. The scores differ, depending on which acquisition strategy was used: NonCleavable, NonCleavable_fast, MS2, MS2_MS2, MS2_MS3, or MS2_MS2_MS3. The higher the score, the better the match is. For information on these strategies, see XlinkX/PD Detect node. |
ΔM [ppm] | Displays the difference between the theoretical mass of both crosslinker peptides and the experimental mass of the precursor ion. |
# Proteins | The total number of proteins containing the identified CSM. |
Identified by | Indicates if the CSM was identified by the MS2 or the MS3 spectrum. |
Modifications A | The modifications detected on peptide A. |
Modifications B | The modifications detected on peptide B. |
Identifying Node No | The number of the node, which created the identification. |
All Scans: | Scan numbers of all scans that were acquired to identify this scan. |
Mzs A [Da] | All m/z masses for the reporter peaks of peptide A |
Mzs B [Da] | All m/z masses for the reporter peaks of peptide B |
Charges A | All charge values for the reporter peaks of peptide A. |
Charges B | All charge values for the reporter peaks of peptide B. |
Spectrum File | The file name in which the CSM was identified. |
File ID | The short identifier of the input file from which the CSM was received. |