Questions tagged [mass-spectrometry]

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Seeking Advice on Acquiring Clean Experimental data comprises of proteins for FDR Estimation

I am a bioinformatics student doing my research on top-down mass spectrometry-based proteomics and seeking some guidance on acquiring very clean experimental data with known true positives and false ...
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Finding mutations in glycosylation sites

We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio). Counting the number of tandem repeats is a ...
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Mass spectrometry: How to obtain expression counts for protein

I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent. Each sample corresponds to a folder ...
FalleS's user avatar
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Gene/protein expression specific to a group in omics

I am wondering what is the significance of finding a particular protein specific to a disease or control group? when we detect 1000s of proteins in a proteomics experiment, how can one be sure that ...
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Heat map of protein expression from normalized abundance

This is a follow up to my question posted here Processing proteomics data In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
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Processing proteomics data

[this question was also asked on BioStars] In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked ...
Natasha's user avatar
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Why does this modification site file contain duplicate sites and multiple related proteins?

The data below is coming from a MaxQuant post-translational protein modification (PTM) site file. Why does it contain duplicate sites (yellow) and proteins (cyan)? Source data http://ftp.ebi.ac.uk/...
Kermit's user avatar
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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 ...
FJ_nw's user avatar
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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 ...
There's user avatar
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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 ...
webNoob13's user avatar
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Hybrid approach in metabolomics (NMR and MS) [closed]

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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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 ...
Manuel's user avatar
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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?
Soerendip's user avatar
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3 votes
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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 ...
Osaama Shehzad's user avatar
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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 ...
Soerendip's user avatar
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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 ...
Soerendip's user avatar
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5 votes
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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 ...
Soerendip's user avatar
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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 ...
virtualxtc's user avatar