4
votes
Accepted
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 (...
- 19.5k
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.
- 146
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.
- 1,139
2
votes
Accepted
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 ...
- 1,285
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 ...
- 4,174
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.
...
- 1,285
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 ...
- 246
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.
- 111
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__♦
- 11.2k
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 ...
- 131
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,...
- 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 ...
- 36
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__♦
- 11.2k
Only top scored, non community-wiki answers of a minimum length are eligible