How do I make a ProteomeXChange complete submission (not partial) with MaxQuant-searched proteomics data?

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Yasset Perez-Riverol Popular answer

Dear all: I'm the PRIDE Coordinator. We recently implemented the support for MaxQuant complete submissions in mzTab. You can download the latest version of MAxQuant and perform the submission. Please let us know if you need any support.

Simon Gregersen

Hi Tue

Just got back from the MQ SummerSchool and this topic was discussed. As I remember it, all MQ results are unfortunately only possible to upload as partial entries to PRIDE, but the MQ team is working on it. You can check out the lecture from Barcelona (15 minutes) using the link below.

https://www.youtube.com/watch?v=4qvOtXy-uoI

Tue Bjerg Bennike

Perfect. Thank you very much Simon!

Edward Emmott

I did hear that you can actually do a complete submission to ProteomeXchange if you do it via Massive rather than through PRIDE, though haven't yet done this myself.

https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp

Thank you Edward Emmott. I will check if that is an option.

Varshasnata Mohanty

Hi Tue Bjerg Bennike,

You can try coverting your result files from MaxQuant to mzIdentML or PRIDE XML format using MS-viewer and try uploading the same using PX submission tool which allow the option for both partial and complete submission. I have attached the manual for the same (Go to Page 6). I hope it helps.

Thanks!

Hi The

In the new version of MQ, the issue is resolved and you can now write MZtab files directly for full submission in PRIDE.

https://groups.google.com/forum/m/#!topic/maxquant-list/tjNWWs2S5sk

Cheers,

Simon

Dear Varshasnata Mohanty and Simon Gregersen ,

Thank you both for your valuable answers!

/Tue

Yasset Perez-Riverol

Michael Plank

Hi,

does anyone have a suggestion for data upload from a MaxQuant version before mzTab was implemented?

I tried upload at Massive, but it always fails with an error. With MS-Viewer I can generate a table, but don`t see a way how to download it as PRIDE xml or similar.