Datasets from SIM-XL, Mascot and ProteomeDiscover in PRIDE

[ypriverol]

We have to find out the list of datasets with the following conditions:

• mzIdentml 1.2 (Complete submission)
• Peak list files corresponding to the mzid
• Software that produces the files ProteomeDiscover / Mascot / SIM-XL
• Crosslinking (this is the most important one )

Please lets update the list in this issue.

[sureshhewabi]

Datasets in PRIDE with "crosslink" or "cross-link" word in TITLE which contains mzIdentML files:

Ordered by priority:

• PXD029252, Proteome Discoverer - Failing - No mgf presents
• PXD021417, TOPP software - Datasets from SIM-XL, Mascot and ProteomeDiscover in PRIDE #63 (comment)
• PXD014359,TOPP software - Datasets from SIM-XL, Mascot and ProteomeDiscover in PRIDE #63 (comment)
• PXD014520,TOPP software - spectra ref to Raw files
• PXD014523,TOPP software - Spectra Location Unknown
• PXD026603, ProteomeDiscover - Datasets from SIM-XL, Mascot and ProteomeDiscover in PRIDE #63 (comment)
• PXD028039, xiFDR software: Failing no mgf
• PXD050457, MassIVE dataset, looks like it works in xiView
• PXD018935,Proteome Discoverer
• PXD012759,Proteome Discoverer

Need to check version 1.2, the corresponding peak list and producer

[colin-combe]

as noted in meeting, they might not be complete submissions
(what does the strikeout represent above? PXD018935 / PXD012759)

[colin-combe]

"crosslink" or "cross-link" word in TITLE

wasn't there a "crosslink" tag people were referring to? (I don't know but people spoke of this)

[ypriverol]

We will continue with different combinations. We will et you know when errors start to happen.

[colin-combe]

OK, great, thanks!

[ypriverol]

@sureshhewabi reported the following error in this one:

PXD014359 - Error parsing C_Lee_141014_CRM_dialysis_NCE20_2.mzid
MzIdParseException ('XMLSyntaxError', ("Start tag expected, '<' not found, line 1, column 1",))
2024-04-04 09:35:10 - main - ERROR - ('XMLSyntaxError', ("Start tag expected, '<' not found, line 1, column 1",))

[colin-combe]

i guess the error message is correct and it is not valid XML

[ypriverol]

Another similar error for OpenMS

Error parsing XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzid
MzIdParseException ('XMLSyntaxError', ("Start tag expected, '<' not found, line 1, column 1",))
2024-04-04 14:28:13 - parser.process_dataset - ERROR - ('XMLSyntaxError', ("Start tag expected, '<' not found, line 1, column 1",))

[sureshhewabi]

Schema seems valid in XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzid file from PXD021417:
xmllint --noout --schema mzIdentML1.2.0.xsd XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzid > XLpeplib_Beveridge_QEx-HFX_DSS_R1_output_file1.txt 2>&1

There should be an issue with the parser. @colin-combe any idea?

[colin-combe]

yes, could be a issue with parser. Or perhaps something to do with character encoding. I looked into and was confused.

@sureshhewabi - I'm not sure what your xmllint command does ?

[sureshhewabi]

It is a command to check the schema validity against the schema definition file(xsd)

[colin-combe]

one problem is the empty location attribute for spectra data:

XLpeplib_Beveridge_QEx-HFX_DSS_R3.mzid, line 527672:
<SpectraData location="" id="SDAT_1534307058980521776">

It is a required attribute, but empty string is enough to make the file schema valid (http://www.datypic.com/sc/xsd/t-xsd_anyURI.html).

But this isn't the only problem, there's something else that's still mysterious...

[sureshhewabi]

This means we cannot use this dataset for us anyway, isn't it? because we cannot find the peaklist file