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4 votes
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Running MaxQuant on Linux

There is a conda package for maxquant that should work on most platforms (I've used it on CentOS and I think it's been used on Ubuntu as well). There's also a docker container version of that that we (...
Devon Ryan's user avatar
  • 19.6k
3 votes
Accepted

How to run proteowizzard on linux using wine?

Try this Docker container. All the vendor formats work except T2D, YEP, and FID.
Matt Chambers's user avatar
2 votes
Accepted

How to run MaxQuant in command line mode?

Give mono MaxQuantCmd.exe [OPTIONS] a try. University of Oslo description of how to use the tool in their infrastructure.
Kohl Kinning's user avatar
  • 1,149
2 votes
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Principle of TMT Tags in Multiplex Proteomics

TMT stands for tandem-mass-tag. The idea is to tag different samples with one of the tags then pool all samples together and run them through the mass spectrometer together. Then the reporter groups ...
Soerendip's user avatar
  • 1,295
2 votes

Why does this modification site file contain duplicate sites and multiple related proteins?

There are multiple protein isoforms that the gene may encode. The hyphen-number after the Uniprot ID represents the isoform —in a Uniprot you find the detail of these at the bottom. The canonical ...
Matteo Ferla's user avatar
  • 4,234
2 votes

Running MaxQuant on Linux

I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install mono. ...
Soerendip's user avatar
  • 1,295
2 votes

Gene/protein expression specific to a group in omics

You can never be 100% sure that a difference is real and not a statistical fluke. This is the entire concept underlying Type I errors - these are errors where the null hypothesis (usually, that there ...
Nuclear Hoagie's user avatar
1 vote

Heat map of protein expression from normalized abundance

The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.
Pete Kittinun's user avatar
1 vote

Processing proteomics data

You asked two questions Is it possible to find from the dataset (i.e does the raw file contain information on the sample whether it is a diabetic sample or a control sample?). Should the diabetic and ...
M__'s user avatar
  • 12.5k
1 vote

Why does this modification site file contain duplicate sites and multiple related proteins?

According to a proteomics researcher at the NIH: proteins column contains uniprot IDs. position within proteins column are the ...
Kermit's user avatar
  • 131
1 vote

Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)

Regarding the big FC values, I just realise the Limma lmfit function requires as input a log2 matrix... so I just transformed my data and now makes more sense. Still I have the doubt regarding the ...
FJ_nw's user avatar
  • 31
1 vote

Bruker MALDI-TOF bacteria species identification scoring algorithm

For identification scoring, the software correlates signal intensities of matched signals of mass spectra. The three scores obtained from such a procedure are multiplied and normalized to a value of 1,...
There's user avatar
  • 151
1 vote
Accepted

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

In a peptide tandem mass spectrometry experiment, each fragment (child) ion is typically the result of breaking a single bond in the peptide backbone yield b and y ions. Because each ion fragment ion ...
Will Fondrie's user avatar
1 vote

How to run proteowizzard on linux using wine?

I sympathize ... If it is a Mac just run 'PlayonMac' its a brilliant frontend for Wine without all the bugs and hassles it causes. Its free and available here
M__'s user avatar
  • 12.5k

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