I'm having a problem with my current Maxquant files: when comparing to the peptide counts and number of proteins of the same sample, Maxquant finds a lot less than Mascot

(about half for both).

The guy who does my MS measurements works at a different institute and they are using Mascot there but for me MaxQuant is more convenient as it is free and i have some knowledge about how to use it.

My Maxquant version number is v2.0.0.

I ran all my samples with the default settings so he said i should change the MS1 search to 5 ppm and the ms2 search to 0.6 Da as these samples were analysed by Orbitrap MS and IT HCD MSMS. Unfortunately I am not sure which parameters should be adjusted in Maxquant (I tried the 'MSMS analyzer/IT MSMS mass tolerance' adjustment to 0.6Da but i dont know if i should change the 'de novo' tolerance too. Also, I tried to change the settings for 'Instrument/Orbitrap' but none had any significant effect).

I tried to check the output files and for some reason in MSMS.txt it says that the Frangentation is CID, not HCD. I dont know why...

I really dont know how i should adjust the program to provide similar peptide counts and protein numbers. I'd like to continue using Maxquant as I want to use the LFQ normalization method from it.

If you have any comments/ideas on this issue, please dont hesitate to write. All pieces of advice is highly appreciated.

Best regard,

Peter