10000 No IMS model ran mzML input · Issue #117 · lazear/sage · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

No IMS model ran mzML input #117

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
patrick-willems opened this issue Feb 5, 2024 · 5 comments
Closed

No IMS model ran mzML input #117

patrick-willems opened this issue Feb 5, 2024 · 5 comments
Labels
bug Something isn't working

Comments

@patrick-willems
Copy link

Hey,

I was eager to test the new ims model on some of our data. I use MS2-only mzML files that contain ion mobility fields as:

<cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.1835660934448242"/>

After succesfully running sage, the PIN and TSV outputs the ion_mobility, predicted_mobility and sqrt(delta_mobility) columns all default to zero for all PSMs. Do we need to specify another JSON parameter or the info might not be correctly parsed from the mzML?

Thanks!
@lazear
Copy link
Owner
lazear commented Feb 5, 2024

Can you share which converter you used, and the mzML for the full spectrum (or the whole file)? I am going to guess that this has to do with IMS being written to different parts of the XML document by different converters.

@lazear lazear added the bug Something isn't working label Feb 5, 2024
@patrick-willems
Copy link
Author

These files were converted by MSFragger. The gzipped mzML can be downloaded via: https://filesender.belnet.be/?s=download&token=0f657e1d-ea0c-4c75-8b89-227cf2d1394c

Random example spectrum:

<spectrum index="18851" id="controllerType=0 controllerNumber=1 scan=18874" defaultArrayLength="207" dataProcessingRef="MSFragger">
          <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/>
          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
          <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="720.385009765625" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="3636.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="16334.0"/>
          <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="199.143798828125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1539.11572265625" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
          <cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="T05451_AurEl4_PM2_CMB-1482-MHCI_new_GB3_1_6084.18874.18874.1"/>
          <userParam name="uncalibrated precursor mz" value="720.37695"/>
          <scanList count="1">
            <scan>
              <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="19.516155242919922" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
              <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.2539584636688232"/>
              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value=""/>
              <scanWindowList count="1">
                <scanWindow>
                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="199.143798828125" unitCvRef="MS" unitAccessi
8000
on="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1539.11572265625" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                </scanWindow>
              </scanWindowList>
            </scan>
          </scanList>
          <precursorList count="1">
            <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=10898">
              <isolationWindow>
                <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="720.657615" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.1076272070312143" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="1.1023947656250357" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                <userParam name="ms level" value="1"/>
              </isolationWindow>
              <selectedIonList count="1">
                <selectedIon>
                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="720.3768122581744" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
                  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="5823.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
                </selectedIon>
              </selectedIonList>
              <activation>
                <cvParam cvRef="MS" accession="MS:1000044" name="UNKNOWN" value=""/>
              </activation>
            </precursor>
          </precursorList>
          <binaryDataArrayList count="2">
            <binaryDataArray arrayLength="207" encodedLength="1064">
              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
              <binary>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</binary>
            </binaryDataArray>
            <binaryDataArray arrayLength="207" encodedLength="572">
              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
              <binary>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</binary>
            </binaryDataArray>
          </binaryDataArrayList>
        </spectrum>

@jspaezp
Copy link
Contributor
jspaezp commented Feb 5, 2024 •
edited
Loading

ok ... the issue is that I was expecting the 1/k0 info to be inside the selected ion info

              <selectedIonList count="1">
                <selectedIon>
                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="720.3768122581744" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="1"/>
                  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="5823.0" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
                </selectedIon>
              </selectedIonList>

whilst in your data it is located in the scan info

          <scanList count="1">
            <scan>
              <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="19.516155242919922" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>
              <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.2539584636688232"/>
              <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value=""/>
              <scanWindowList count="1">
                <scanWindow>
                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="199.143798828125" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="1539.11572265625" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                </scanWindow>
              </scanWindowList>
            </scan>
          </scanList>

... I think according to the current mzML specification both are viable annotations, it is both a:

  1. ion mobility attribute -> scan attribute
  2. ion selection attribute.

https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo line 18481

The solution would be to copy the content here:
https://github.com/jspaezp/sage/blob/a7414c8bcf608c5b5ff5271c08d1f5d87d72c23b/crates/sage-cloudpath/src/mzml.rs#L241-L243

to this line as well ...

https://github.com/jspaezp/sage/blob/a7414c8bcf608c5b5ff5271c08d1f5d87d72c23b/crates/sage-cloudpath/src/mzml.rs#L263

IN THE MEANTIME you can pass the .d directly! (if you have one ...)

@jspaezp
Copy link
Contributor
jspaezp commented Feb 5, 2024

#119

(possible) fix there

@patrick-willems
Copy link
Author

Thanks for the help! I can work with this.

@jspaezp jspaezp mentioned this issue Feb 6, 2024
Merged
This was referenced Feb 9, 2024
Closed
Closed
@lazear lazear closed this as completed Mar 15, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@jspaezp @lazear @patrick-willems
0