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Description
Objective:
Use target decoy competition (tdc) to select one PSM per scanNr per rawfile, irrespective of expMass.
Problem:
tdc uses scanNr+expMass to identify PSMs that should be considered to originate from the same spectrum.
When having no expMass column but multiple RAW files, this is creating an issue because unrelated PSMs from different RAW files that share the same ScanNr are considered to originate from the same spectrum!
A dirty workaround is to utilize the expMass column by simply grouping filename+scanNr and assigning an increasing number to these groups, i.e.:
filename, scannr, expMass
file1, 100, 1
file1, 100, 1
file2, 100, 2
file2, 100, 2
In this example, scannr 100 is now correctly separated between filenames because the "expMass" is different. This works, but is a bit hacky...
Desired behaviour:
tdc should always be based on filename+scanNr+expMass. This doesn't affect the current behaviour when expMass is provided, so it should be an easy fix.