Questions tagged [mass-spectrometry]
The mass-spectrometry tag has no summary.
19 questions
1 vote
1 answer
40 views
Is it possible to obtain the sequences from polyclonal antibody protein mixture via mass spec? [closed]
We have been using pAbs from an immunized goat for quite a few years but now the goat died. We only have the antigen affinity purified pAb proteins. Is it possible to obtain the sequences? We have ...
- 11
2 votes
1 answer
66 views
What parameter and threshold to choose to get significant pathways from MetaboAnlyst pathway analysis results?
MetaboAnalyst pathway analysis results give a total of 4 different p-values viz, raw p-value, -log10 pvalue, Holm-Bonferroni adjusted p-value and the FDR value. And an impact score. Which value should ...
- 21
1 vote
0 answers
51 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 ...
- 2,242
1 vote
0 answers
34 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 ...
- 11
1 vote
1 answer
54 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 ...
2 votes
1 answer
2k 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 ...
- 125
3 votes
1 answer
903 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 ...
- 125
2 votes
2 answers
49 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/...
- 131
2 votes
1 answer
246 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 ...
- 31
4 votes
1 answer
1k 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 ...
- 151
1 vote
1 answer
42 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 ...
- 145
1 vote
0 answers
49 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 ...
- 11
2 votes
2 answers
4k 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 ...
- 123
1 vote
1 answer
65 views
Can Maven (mass spectrometry software) read mzML files?
I did not find a documentation. Can Maven (mass spectrometry software) read mzML files?
- 1,315
3 votes
1 answer
1k 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 ...
- 103