The Crosslinks page displays the grouped crosslinks. Crosslinks are created by grouping all CSMs that identify the same crosslink. Crosslinks are grouped on the basis of the position of the chemical crosslink in the sequence of the protein or proteins. This results in crosslinks containing CSMs with different side chain modifications and even different lengths of the peptides identified with the crosslink. The sequences of the two crosslinked peptides in the table show the longest available sequence identified in the associated CSMs.
Spectrum-specific values (for example, the identification details of single peptide of a crosslink in an MS3 spectrum) of MS2 scans and MS3 scans that were used to identify the CSM are shown in the Crosslink MS2 Scans and Crosslink MS3 Scans table. To use the spectrum data for a specific CSM, select Show Associated Tables to obtain the scan information for each spectrum that was measured for the CSM.
For information about the quantitation results columns, refer to the section, “Interpreting Quantitative Results,” in the Proteome Discoverer User Guide.
The following figure gives an example of the Crosslinks page.
The following table describes the columns on the Crosslinks page of the result file.
Column | Description |
|---|---|
# CSMs | Displays the number of crosslink spectrum matches identified for the crosslinker. |
Accession A | Displays the accession number of the first identified protein that contains the crosslinker. |
Accession B | Displays the accession number of the second identified protein that contains the crosslinker. |
Checked | Indicates whether the item is selected. |
Confidence | Displays the level of confidence in the crosslink identification. |
Crosslink localization probability | Indicates probability of the crosslink site identification. |
Crosslink Type | Displays the type of crosslinked peptide:
|
Crosslinker | Displays the name of the crosslinker used. |
Max. 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 used: NonCleavable, MS2, MS2_MS2, or MS2_MS3. The higher the score, the better the match is. For information on these strategies, see Activate the license. |
# Proteins | Number of identifies proteins in which the Crosslink or one of its peptides is contained. |
Crosslink Sequence: | A display of the connected peptides in the crosslink. |
Modifications A | Modifications found in Peptide A of the crosslink. |
Modifications B | Modifications found in Peptide B of the crosslink. |
Position A | Displays the position of the crosslink in the first protein. |
Position B | Displays the position of the crosslink in the second protein. |
Protein Descriptions A | Displays a description of the first protein that contains the crosslinked peptides. |
Protein Descriptions B | Displays a description of the second protein that contains the crosslinked peptides. |
Sequence A | Displays the amino acid sequence of the first peptide in the crosslink. The site of the crosslink appears in brackets. |
Sequence B | Displays the amino acid sequence of the second peptide in the crosslink. The site of the crosslink appears in brackets. |