Any possiblity to require users to upload correction factors for TMT data in PRIDE?

[JinqiuXiao]

Hi everyone,

Our group is recently working with TMT datasets from published data. When we search for the dataset, we found that very few research provide the imputrity correction factors for the TMT dataset in the article, which made it impossible to reanalyze the data properly.

We're wondering if in the future, it would be possible to require users to provide the impurity correction factors, or the Lot # of the TMT reagent kit, when they upload the TMT dataset to PRIDE? We believe it'll help a lot to improve the reproducibility and reanalysis of the TMT datasets.

Best,
Jinqiu

[ypriverol]

@JinqiuXiao Thanks for contacting the SDRF team. We had a long discussion about how to provide this information. One idea was to attach to the comments in the TMT experiments the file with the impurity correction factors but we were not 100% sure how we should capture/model the file itself. Do you have ideas? Can you provide one example? Are you interested in working with us to model within the SDRF community?

[JinqiuXiao]

Hi @ypriverol,

Sorry for the late reply, last week we were busy with the MaxQuant summer school. The simplest solution in my opinion would be to include a column refereing to the Lot Number of the TMT reagent(s), which can be used to query the correction factors from the reagent provider (eg. Lot # ZH389350). This way, you don't have to change the structure of the sdrf for TMT, and it's also not much work for other users to query.

Exporting the sdrf with MaxQuant is on our list, but we're not currently working on it. When we start to implementing it, we would be very glad to get suggestions from you!

Best,
Jinqiu

[ypriverol]

I actually was thinking more like in an external file. In the comment section of the SDRF provide a name of the file to TMT internal calibrations and then, define that file. Can you send me an example file that you use in MQ as input? @timosachsenberg may also can help about the file input that OpenMS uses.

[JinqiuXiao]

Sure, here you can find a template of the impurity correction factors for TMTpro 16plex in MQ. You can export the templates for all other TMT plexes by selecting them and clicking "Export" as shown in the screenshot.

[ypriverol]

Great we will start working with this file.

MQ_TMTpro16.txt