what do you use for proteomics downstream analysis:

Moving forward with the idea of proteomics pipelines in the cloud, collaboration with @OpenMSTeam. Label-free pipelines in development using @nextflowio @nf_core @BioContainers @OpenMSTeam #MSstats #SDRFproteomics

Thanks to @JohnRYatesIII and @JProteomeRes for the invitation to publish a perspective on sample metadata in public repositories pubs.acs.org/doi/abs/10.1021… , Thanks to all @EuBIC_ms contributors. Since the publication, we have opened 10 new PRs in the repo github.com/bigbio/proteomics…

Sample metadata in Proteomics repositories youtube.com/watch?v=ybueEagj… github.com/bigbio/proteomics… a project from @EuBIC_ms

While in genomics + transciptomics everyone is in conda + containers. In proteomics, we can't distribute the software without clicking a license page. New tool MutCombinator following the same style... I don't know how the field will move to large-scale data analysis.

For those that would like to know more about SDRF here the link to the @EuBIC_ms Hackathon eventbrite.co.uk/e/eubic-hac… RT !!!! #ASMS2020 #proteomics @ProteomeXchange

You can register for the Hackathon next week on Sample metadata annotations hosted by @EuBIC_ms.

If you are wondering how to sample annotations will look like in Proteomics. Here an example of the first annotated submission in @pride_ebi with Sample annotations from @GygiLab ebi.ac.uk/pride/archive/proj… . All the annotations have been done based on SDRF (github.com/bigbio/proteomics…)

Online Hackathon and Workshop about the sample to data file format (SDRF) in proteomics. @EuBIC_ms #HUPOPSI @pride_ebi @ExpressionAtlas eventbrite.co.uk/e/eubic-hac….

Thanks to @ExpressionAtlas Team for their support. Anja Fullgrabe @pabloOmics and @irenepapatheodo.

Thanks to @EuBIC_ms the new SDRF file format for proteomics is really getting adopted. Multiple contributions from @EuBIC_ms members such as @mvaudel @OpenMSTeam @lgatt0 and Lev Levitsky, Johannes Griss github.com/bigbio/proteomics… . We hope more people get involved.

Should we make the experimental design based on the SDRF (sample to a data file format - github.com/bigbio/proteomics…) on each PRIDE submission:

Beta version of an Annotator of the SDRF is now deployed annotator.multiomics.info/ semantic auto-complete of ontology terms.

The specification is here (github.com/bigbio/proteomics…). If you have submitted a dataset to @pride_ebi help us to re-annotate them.

61 projects annotated using the SDRF specification (github.com/bigbio/proteomics…). TMT, SILAC, Label-Free, phospho-proteomics, protein-protein interactions experiments. A validator is now in place, every time a collaborator add a new experiment, the PR will be validate before merge.

Finally out: OmicsDI REST interface academic.oup.com/nar/advance…

What do you think is the next step for proteomics archives?

Great effort from @OpenMSTeam, @MuenchLab, and myself to annotated the SARS-Cov-2 submission Experimental design in SDRF github.com/bigbio/proteomics…