Issue 45621: Parse and report on crosslinkers as modifications

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:TargetedMS
Priority:3
Milestone:22.07
Opened:2022-06-03 16:59 by jeckels
Changed:2022-07-13 16:18 by wendyi
Resolved:2022-06-11 10:52 by jeckels
Resolution:Fixed
Support Ticket: 
Pull Requests:MacCossLabModules#217
targetedms#560
Closed:2022-07-13 16:18 by wendyi
2022-06-03 16:59 jeckels
Title»Parse and report on crosslinkers as modifications
Assigned To»jeckels
Notify»Keith
Type»Defect
Area»TargetedMS
Priority»3
Milestone»22.07
This will probably require a minor DB schema change so assigning to 22.7 for the moment.

As discussed on a customer call today, in both the PTM and Peptide Map reports, for cross-linked peptides we're not currently reporting on the crosslinker as a modification. We can get almost everything we need from the modified peptide sequence, but it doesn't contain a reference to the crosslinker definition. That's handled in a separate section of the Skyline XML that we're not currently importing. Example XML snippets (with potentially sensitive info hacked out):

          <static_modification name="Disulfide Linker" aminoacid="C" formula="-H2" explicit_decl="true">
            <crosslinker />
          </static_modification>

    <peptide auto_manage_children="false" sequence="PEPTIDEA" modified_sequence="PEPTIDEA-PEPTIDEB-[-2.01565@4,4][-2.01565@7,7]" start="128" end="154" prev_aa="K" next_aa="D" calc_neutral_pep_mass="543.554" num_missed_cleavages="0" avg_measured_retention_time="45.37">
      <explicit_modifications>
        <explicit_static_modifications />
      </explicit_modifications>
      <crosslinks>
        <linked_peptide sequence="PEPTIDEB">
          <explicit_modifications>
            <explicit_static_modifications />
          </explicit_modifications>
        </linked_peptide>
        <crosslink modification_name="Disulfide Linker">
          <site peptide_index="0" index_aa="3" />
          <site peptide_index="1" index_aa="3" />
        </crosslink>
        <crosslink modification_name="Disulfide Linker">
          <site peptide_index="0" index_aa="6" />
          <site peptide_index="1" index_aa="6" />
        </crosslink>
      </crosslinks>

2022-06-09 15:18 jeckels
Pull Requests»https://github.com/LabKey/MacCossLabModules/pull/217 https://github.com/LabKey/targetedms/pull/560

2022-06-11 10:52 jeckels
resolve as Fixed
Statusopen»resolved
Assigned Tojeckels»Keith
This is now merged to develop and will be part of 22.7.0. In order to see info about crosslinkers as modifications, the Skyline documents will need to be reimported.

2022-07-13 16:10 jeckels
NotifyKeith»Keith;wendyi
In order to see the links for the PTM and Peptide Map reports you must be in a MAM Panorama folder.

https://www.labkey.org/Documentation/wiki-page.view?name=panoMAM