XiFDR mzid files give errors, but CSM files work

[ciancone94]

I have recently been running into a strange issue where the mzid generated from XiFDR (v.2.2.1) when uploaded to XiView gives an error that isn't particularly descript. The XiSearch file was generated using XiSearch v1.8. Here is the error I get when I load the page:

An error has occurred. ☹

value@https://xiview.org/dist/xiview.js:2:5894699 dc@https://xiview.org/dist/xiview.js:2:6673915 Nc@https://xiview.org/dist/xiview.js:2:6671863 o@https://xiview.org/dist/xiview.js:2:6731063 Sc/<@https://xiview.org/dist/xiview.js:2:6741264 4143/Dt/n.send/<@https://xiview.org/dist/xiview.js:2:2022210 e@https://xiview.org/dist/xiview.js:2:1995932 s@https://xiview.org/dist/xiview.js:2:2021164 Try loading data only.

and here is the error when I first try uploading the mzid:

log id: 0r2n4rmikr078db3sb8i2of2al_1712239173.log (include this in the github issue) error type: Error message: name id: undefined

The strangest thing is that this is only sometimes an issue for some datasets but not others (when generated from the same versions of XiSearch and XiFDR). Perhaps it has something to do with the configs? Here is the config: SDA_InVitro_OandNGlycosylations_240401.txt

Please note that uploading the CSM for this dataset works without error.

Thank you,

Anthony

[colin-combe]

Hi Anthony,

An error has occurred. ☹

i should maybe take out that sad emoji, it could get annoying.

the first xiVIEW error will be because of the failure uploading the mzid.

The failure uploading the mzid is perhaps because of empty cvParam elements in the mzIdentML file.

Could you search the mzId file for <cvParam></cvParam>? If you find it then that is the problem and replacing them with empty strings may make it work.

If it is that, then you could comment on this issue - https://github.com/Rappsilber-Laboratory/xiFDR/issues/39

If its not that, then please let me know, cheers, Colin

[ciancone94]

Colin,

Thanks for the quick reply. I replaced all of the with:

and this allows XiView to load in the mzid.

It appears that all of the errors stem from a 25 Da mass that it finds. This is the SDA crosslinker defined as linking a cysteine to a K/S/T/Y or n-term, when Ccm is defined as a fixed mod:

crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:SDACcm;MASS:25.02040084;FIRSTLINKEDAMINOACIDS:Ccm;SECONDLINKEDAMINOACIDS:K,S,Y,T,nterm

So perhaps this error only gets thrown when XiView runs into this XLer mod; however, I don't know why this would happen, as this is the typical syntax for a crosslinker mod in the config.

Anyways, thanks for the help. Maybe Lutz or Andrea will know what I am doing wrong here with the config.

Thank you,

Anthony