Spectral library building from MaxQuant msms.txts | danielz | 2018-07-13 05:56 | |||||||||||||||||||||
Dear Skyline team, foremost thank you very much for providing such a tool to the community. MaxQuant does a lot of peak processing on the original raw scan, i.e. it tries to decharge multiply charged fragment ions if also a 1+ version of the fragment is detected. This does basically no harm to 2+ precursors, but for precursors with z>= 3+ a lot of times it means that the spectrum that is stored in the MaxQuant .res files as well as all fragment m/z information that is written as annotated peaks to the msms.txt file does not represent what the raw scan looked like. As the decharging of spectra cannot be disabled in MQ, my current workarounds are a) use Mascot/Sequest/EngineXYZ where you can control this parameter (by then potentially imparing the DDA data search through noisier and more complex MS2 spectra). Or b) you extract the raw scans yourself, manually or using some implementation of the ThermoRAWFile Reader library. My question is a) are you aware of this, b) is this recognized as a problem and c) are there plans to integrate such functionality or is the direct import of spectral libraries from MaxQuant files anyway only used by a low proportion of users, because most spectral libs come from different tools/sources? Best, |
|||||||||||||||||||||||
| |||||||||||||||||||||||