Questions tagged [mass-spectrometry]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
1 vote
0 answers
37 views

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 ...
Angel's user avatar
  • 1,981
1 vote
0 answers
22 views

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
  • 11
1 vote
1 answer
37 views

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 ...
Balasubramaniam Namasivayam's user avatar
2 votes
1 answer
911 views

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 ...
Natasha's user avatar
  • 125
3 votes
1 answer
412 views

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
  • 125
2 votes
2 answers
35 views

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
  • 131
1 vote
1 answer
131 views

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
  • 11
4 votes
1 answer
441 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 ...
There's user avatar
  • 151
1 vote
1 answer
21 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 ...
webNoob13's user avatar
  • 145
1 vote
0 answers
30 views

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 ...
Garrus990's user avatar
1 vote
2 answers
3k 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 ...
Manuel's user avatar
  • 113
1 vote
1 answer
35 views

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
  • 1,295
3 votes
1 answer
567 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 ...
Osaama Shehzad's user avatar
1 vote
0 answers
144 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 ...
Soerendip's user avatar
  • 1,295
0 votes
2 answers
200 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 ...
Soerendip's user avatar
  • 1,295
5 votes
2 answers
4k 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 ...
Soerendip's user avatar
  • 1,295
1 vote
0 answers
22 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 ...
virtualxtc's user avatar