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baynec2 / mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data
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quality score differences #8

Open baynec2 opened 1 month ago

baynec2 commented 1 month ago

There are differences in the quality metrics used by proteome discoverer and PEAKS. Take a look into this.

baynec2 commented 1 month ago

currently, this effects how things are filtered out. The proteome discoverer quality scores are systematically lower than what is reported in PEAKs. Functionally this means nothing gets filtered out from proteome discoverer at the moment.

It might be worth looking into these differences and if we can convert to a standard value.