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Milestone - Metaproteomics workflow updated to remove matched metagenome requirement (2.14.2) DUE #455

Open ssarrafan opened 10 months ago

ssarrafan commented 10 months ago

Expanding the metaproteomics workflow There are two limitations of the current metaproteomics workflow that limit its utility for the community, (i) peptide sequence identification currently requires a matched metagenome for streamlined query, and (ii) all data sets are treated independently which precludes sample comparisons by relative quantitation. To provide an alternative workflow that removes the requirement for a metagenome, the metaproteomics workflow will use an EMSL developed tool75 that uses a machine learning model to identify peptide sequences de novo, and then uses these sequences to predict taxonomy and derive a pseudo-metagenome for use as the input database (Milestone 2.14).

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ssarrafan commented 7 months ago

Rescheduled for Q4 of this year per the milestones spreadsheet.

Also renamed: (MODIFIED) Modify reference metagenome-independent metaproteomics workflow; retrain the peptide-spectrum ML model, and redesign protein sequence database generation

aclum commented 1 month ago

per checkin meeting @picowatt thinks we are on track for this quarter. cc @SamuelPurvine