Omics Discovery

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/10.102… , Thanks to all @EuBIC_ms contributors. Since the publication, we have opened 10 new PRs in the repo github.com/bigbio/proteom…

About half of #systemsbiology models fail to directly reproduce #simulation results! Over the past 3 years we investigated >450 models published in 152 journals & identified the root cause for the lack of #reproducibility. Read our #biorxiv_sysbio article doi.org/10.1101/2020.0…

Sample metadata in Proteomics repositories youtube.com/watch?v=ybueEa… github.com/bigbio/proteom… 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.

The @BioContainers Registry is a light-metadata interface to quickly find the tool and the corresponding container (biocontainers.pro/#/registry). You can get info about NAME, Number of downloads, short description, License. What other information you would like to see?

For those that would like to know more about SDRF here the link to the @EuBIC_ms Hackathon eventbrite.co.uk/e/eubic-hackat… 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/… . All the annotations have been done based on SDRF (github.com/bigbio/proteom…)

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-hackat….

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/proteom… . 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/proteom…) 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/proteom…). 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/proteom…). 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-ar…

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/proteom…