I'm converting RAW files from an Orbitrap Fusion Lumos to mzML and I realized that I'm losing a lot of sensitivity after aplying the PeakPicking filter. Our samples are a peptide mix of isotopologues (here for more info). For instance:
1) Peptide intensity with m/z = 428.2738 (RAW file viewed with Skyline):
As can be seen, with the last conversion I lose about one order of magnitude. So my question is whether is possible to apply this filter without losing sensitivity.
You should compare the shape of the chromatographic peaks before and after peak picking. If the shapes are conserved, this change of scale is nothing to worry about. Some vendors change the intensity calculation when doing peak picking (and you have Thermo doing the peak picking, not ProteoWizard). If you're trying to do absolute quantitation, then maybe you can just scale all intensities by some ubiquitous peak?
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Dear ProteoWizard team,
I'm converting RAW files from an Orbitrap Fusion Lumos to mzML and I realized that I'm losing a lot of sensitivity after aplying the PeakPicking filter. Our samples are a peptide mix of isotopologues (here for more info). For instance:
1) Peptide intensity with m/z = 428.2738 (RAW file viewed with Skyline):
https://imgur.com/X8FPiHW
2) Same peptide intensity after msconvert (--32 --mzML --zlib):
https://imgur.com/w404p8C
3) And same peptide again after msconvert with PeakPicking (--32 --mzML --zlib --filter "peakPicking true 1-"):
https://imgur.com/sZziDb9
As can be seen, with the last conversion I lose about one order of magnitude. So my question is whether is possible to apply this filter without losing sensitivity.
Thank you.
PS: msconvert version:
ProteoWizard release: 3.0.11626 (2017-12-7)
ProteoWizard MSData: 3.0.11623 (2017-12-6)
ProteoWizard Analysis: 3.0.11623 (2017-12-6)
Build date: Dec 8 2017 00:20:05
--
Roger Olivella
CRG/UPF Proteomics Unit
CRG - Centre for Genomic Regulation
Dr. Aiguader, 88
08003 Barcelona (Spain)
Tel.: +34 93 316 08 69
Email: roger.olivella@crg.eu
You should compare the shape of the chromatographic peaks before and after peak picking. If the shapes are conserved, this change of scale is nothing to worry about. Some vendors change the intensity calculation when doing peak picking (and you have Thermo doing the peak picking, not ProteoWizard). If you're trying to do absolute quantitation, then maybe you can just scale all intensities by some ubiquitous peak?