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Missing Peak List File [read Proteome Discoverer export] #17

Closed rchill14 closed 2 years ago

rchill14 commented 6 years ago

We're working with data searched by xlinkx in Proteome Discoverer. Direct exports utilizing any combination of mgf/mzML for peak list do no work here (or zipped), giving the same error message. We also tried searching this without the peak list file, only for it to fail after "updating our ions". The peak list error message is shown below.

Thanks!

Ryan

log id: o2sif9l5op3cbmpv8qafcfuqc3_1536277910.log (include this in the github issue) error type: Error message: Missing peak list file: ../uploads/o2sif9l5op3cbmpv8qafcfuqc3/20180902_AIssaian_Pentamer_DSSO_MS2-(1).zip_unzip/20180902_AIssaian_Pentamer_DSSO_MS2-(1).mzML id: undefined

rchill14 commented 6 years ago

Alternatively with a different file: log id: o2sif9l5op3cbmpv8qafcfuqc3_1536340266.log (include this in the github issue) error type: Error message: ascii id: undefined

colin-combe commented 6 years ago

the first case was maybe the mgf peak list being supplied when the identification file referred to the mzml file.

the second case was maybe the mzml file being supplied but there was a problem reading it. We will update the parser so it either works or provides a meaningful message about what went wrong.

I think reading Proteome Discoverer mzIdentML export won't work because it doesn't export cross-linked peptides in mzIdentML (it exports mzIdentML v1.1).

The xiNET CSV export from Proteome Discoverer possibly does work but is missing the information to make the connection to the peak list files/spectra (but you should be able to look at the network in 2d & 3d).

rchill14 commented 6 years ago

Hi Colin,

Hope you enjoyed some time off and thank you for your explanations. So from what I gather, there really isn't a good way to get xlinkx data from Proteome Discoverer (with spectra) to work here? The 2d and 3D networks are certainly helpful though, so thank you for your efforts here!

Cheers,

Ryan

On Wed, Sep 19, 2018 at 7:05 AM Colin notifications@github.com wrote:

the first case was maybe the mgf peak list being supplied when the identification file referred to the mzml file.

the second case was maybe the mzml file being supplied but there was a problem reading it. We will update the parser so it either works or provides a meaningful message about what went wrong.

I think reading Proteome Discoverer mzIdentML export won't work because it doesn't export cross-linked peptides in mzIdentML (it exports mzIdentML v1.1).

The xiNET CSV export from Proteome Discoverer possibly does work but is missing the information to make the connection the peak list files/spectra (but you should be able to look at the network in 2d & 3d).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Rappsilber-Laboratory/xiView_container/issues/17#issuecomment-422795446, or mute the thread https://github.com/notifications/unsubscribe-auth/ApDry2erR0INbAshQwTE4kHwav_Uuq4Uks5uckEugaJpZM4Wd9Rp .

colin-combe commented 6 years ago

So from what I gather, there really isn't a good way to get xlinkx data from Proteome Discoverer (with spectra) to work here?

Yes, that's right.

You can read the CSV export to get 2d and 3d networks, but there isn't a way to link the supporting spectra.

Ideally, PD would implement mzIdentML v1.2 export

colin-combe commented 2 years ago

I think PD does now have mzIdentML 1.2.0 export