Questions tagged [mass-spectrometry]

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Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)

I am trying to learn how to analyse normalised DIA-MS data and I am struggling with it :// The original dataset I got is (6 conditions (2 samples each)) with 3 technical replicates (total: 36 sample ...
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Hybrid approach in metabolomics (NMR and MS)

Is it currently common in metabolomics to combine two quantification methods, namely NMR (nuclear magnetic resonance) and MS (mass spectrometry, either liquid or gas)? If so, what would be profits ...
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Can Maven (mass spectrometry software) read mzML files?

I did not find a documentation. Can Maven (mass spectrometry software) read mzML files?
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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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How to generate mgf files from Orbitrap generated MS2 proteomics raw files?

I tried to use RawTools to generate MGF files containing peaklists extracted from MS2 mass spectrometry raw-files from an Thermofisher Orbitrap. The command I used was ...
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XCMS isn't evaluating the proper peak due to retention time drift

I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't ...