Vitek-Lab / MSstatsPTM

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments

https://vitek-lab.github.io/MSstatsPTM/

Artistic License 2.0

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fix(pd-converter): Filter out rows without modifications in ptm input #95

Closed tonywu1999 closed 1 month ago

tonywu1999 commented 1 month ago

Motivation and Context

In this google groups post, one user noticed that the PTM input from PD contained un-modified peptides. This should not be the case.

Changes

Filtered out unmodified peptides from the PTM input of the PD converter

Testing

Added unit tests for the PD converter
Added vignette with a global profiling run for the PD converter

Small Todo

I think the converters need some code consolidation. There seems to be a lot of code that does the same thing, but placed in different orders. Ideally, we'd want the converter code to be standardized in a way so that it's easier to create new converters / fix converters in the future.

Checklist Before Requesting a Review

[x] I have read the MSstats contributing guidelines
[x] My changes generate no new warnings
[x] Any dependent changes have been merged and published in downstream modules