Questions tagged [mass-spectrometry]

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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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6 views

How does one go about developing GCMS metabolite annotation workflow?

I’m really new to untargeted metabolomics and I need to annotate a data set from a standard quadrupole GCMS. The person on the project before me tried to do the annotation manually, cleaning up the ...
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2answers
288 views

Running MaxQuant on Linux

I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages I tried to use mono 6.8 mono 5.4.1 on centos ubuntu each with ...
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13 views

Search for XL-MS datasets

I am looking for human cross-linking mass spec datasets, where the exact residues that were crosslinked are stated. Any format, say csv, ...
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1answer
13 views

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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1answer
48 views

Principle of TMT Tags in Multiplex Proteomics

I am new to proteomics research and analyzing mass-spec data. I am trying to learn more about the theory/principle of TMT tagging (a type of isobaric labeling) coupled with LC-MS/MS spectrometry. I ...
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0answers
74 views

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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0answers
31 views

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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2answers
145 views

How to run proteowizzard on linux using wine?

I am trying to run proteowizzard using wine to be able to convert raw mass spectrometry files to myML format. Following, these instructions` which seem terribly outdated. I am getting many issues. I ...
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2answers
2k views

How to run MaxQuant in command line mode?

MaxQuant is a software package for mass spectroscopy and proteomics. There is a windows version and a linux version. To run on linux you have to use a program that is called ...
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0answers
20 views

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 ...