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 ...
3
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1answer
36 views

Bruker MALDI-TOF bacteria species identification scoring algorithm

Just wondering whether anyone can point me to a research paper which describes how the scoring values are generated by the Bruker software for species identification of bacteria in MALDI-TOF MS. For ...
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1answer
18 views

Why don't the "child" peptide masses sum to the parent in this De novo sequencing example?

In that example, 129+216+327 does not equal the parent's mass of 492. My understanding is that during MS, the protein is broken down into peptide masses of varying length of approx. 5 to 20 amino ...
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0answers
26 views

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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2answers
1k 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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1answer
16 views

Can Maven (mass spectrometry software) read mzML files?

I did not find a documentation. Can Maven (mass spectrometry software) read mzML files?
3
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1answer
67 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
101 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
39 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
160 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 ...
5
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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 ...