This is a slightly silly question but we are looking to search fractionated mzMLs using Comet as part of the OpenMS framework. We have 2 choices with Comet:
1. search each fraction mzML in Comet (parallelizing over the fractions) and then merge the results later (the results are idXML files and can be merged using OpenMS's IDMerger)
2. merge the fraction mzMLs first using OpenMS's FileMerger, and search using Comet (once per sample and non-parallel)
When we tested the two options we found that the scores outputted by Comet are different
We were wondering if this is expected and what you would advice on doing: parallel or non-parallel?
Thank you very much!