Error when loading evidence.txt file from MaxQuant 1.6.10.43

[Oana VIGY]

Dear Ulrich,

we faced an error in submitting an "evidence" file from MaxQuant 1.6.10.43 to Protter (same problem on local and online server).

Error: Unmatched closing ')' near index 3 L(M))SFPEAIADCNK

The problem could be due to a changing format which appeared from MaxQuant 1.6.7.0. The oxydation modification in "modified sequence" is for example "_LM(Oxidation (M))SFPEAIADCNK_" and no more "(ox)".

## [1.6.7.0] - 2019-07-10
### Changed
- PTMs in sequence strings are specified by their full name in round brackets, not bei their abbreviations any more. 

Best regards,

Oana

[Ulrich Goldmann]

Dear Oana,

sorry for the very late reply.

You are perfectly right that Protter will not be able to parse this new way of MaxQuant in specifying modifications.

If there is still interest in reading MaxQuant evidence.txt files, I can try to implement support for the new format.

Could you provide me with an example file?

many thanks,

Ulrich

[Oana VIGY]

Dear Ulrich,

thanks for your reply. Yes we're still interested in using "evidence.txt" files with Protter.

I'll share a file in a private message.

Best regards,

Oana

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Oana VIGY

Functional Proteomics Platform (FPP)
IGF, CNRS, INSERM, Univ Montpellier
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Absence: on Mondays

[Alexander Lam]

hello, 

i also have this issue with loading evidence.txt from MQ.