Yasset Perez-Riverol

### Description of feature FLR is the current method Luciphor has to compute the statistics around the phospho sites. However, Luciphor needs 50 PSMs by each charge state to compute...

Update the image of the workflow for DIANN to reflect all the steps in the parallelization

3

### Description of feature Hi @jpfeuffer : At some point, we need to update this figure to reflect the steps of the DIANN pipeline. Even if DIANN is used alone...

MSstats scripts should be merged

2

### Description of feature MSstats scripts for TMT, LFQ and LFQ-DIA shares multiple steps. We should have only one script containing both logics.

### Description of feature Previously in proteomicsLFQ we have a step after the Msstats analysis to "inject" the results of protein/peptide quantification back to mzTab (https://github.com/nf-core/proteomicslfq/blob/43c77e50c955d7e62899e7d31e0d6f6a87ac2316/bin/msstats_plfq.R#L264) However, currently quantms has...

Extending OpenMS for compress support

6

Multiple users are using quantms in AWS for FLQ and TMT analysis. One of the feature requests is to decrease the size of the intermediate files, ideXML, and consensusXML. We...

Would be great to update the following tools to the latest versions COMET, MSGF+, SAGE and Percolator. - Related to issue https://github.com/OpenMS/OpenMS/issues/7498. - https://github.com/bigbio/quantms/issues/393

When given a proforma like: `[+56.026215]-K[+70.041865]SAPSIGGVK[-28.0313]K[+56.026215]PHR/3` the masses returned do not contain the sign if they are positive, the returned proforma is: `[56.026215]-K[70.041865]SAPSIGGVK[-28.0313]K[56.026215]PHR/3` Regards Yasset