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

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

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

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 ...
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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 ...