Questions tagged [maxquant]

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maxquant error: Unhandled Exception: System.IndexOutOfRangeException: Index was outside the bounds of the array

An error occurred while I was running the program maxquant (2.0.3): Reading search engine results (SP) Unhandled Exception: System.Exception: Exception during execution of external process: 1228404 ...
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/...
3 votes
0 answers
130 views

Setting up MaxQuant parameters for processing proteomics data

This is a follow up to my previous question here. 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 ...
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 ...
1 vote
1 answer
110 views

Getting System.IO.FileNotFoundException with MaxQuant running on Linux with mono

I am getting this error with MaxQuant 1.6.14 running with mono (5.14.0.177=he1b5a44_1001). System.IO.FileNotFoundException: Could not find file "/home/ubuntu/run-dir/combined/combinedRunInfo&...
1 vote
1 answer
873 views

What is the purpose of 'Folder locations' in MaxQuant?

MaxQuant is a tool for proteomics quantification. In the settings under Global parameters / Folder locations are three folder locations that are possible to be ...
1 vote
0 answers
50 views

What is the purpose of the "fixedSearchFolder" and "fixedCombinedFolder" in MaxQuant?

What is the purpose of changing the fixedSearchFolder and fixedCombinedFolder in MaxQuant proteomics software? Is there any data ...