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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 (...
Devon Ryan's user avatar
  • 19.6k
2 votes

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

These folders are usually generated in a default directory (where the raw files are). It can however be beneficial to set the paths to these folders manually. Temporary folder that is obviously ...
USER_1's user avatar
  • 121
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
1 vote

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

****this was the xml file that i configured to maxquant. i changed modification and added the fastq and raw file. Other parameters were default. however, 'Unhandled Exception: System....
jing zhao's user avatar
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

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

...seems the mqpar file was not compatible with the maxquant version. Make sure the mqpar.xml file shows the same version number as the MaxQuant binary. ...
Soerendip's user avatar
  • 1,295

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