8  Adapting this workflow to MaxQuant processed data

Learning Objectives
  • Be aware that nomenclature (column names and entries) will differ between software and change over time
  • Know how to edit the code presented in this course to fit with data processed using MaxQuant

8.1 Using data processed with MaxQuant

This course was written for proteomics data processed by the Proteome Discoverer software, as that is what the Cambridge Centre for Proteomics core facility uses to process DDA data (TMT and LFQ). Nevertheless, the workflow and basic principles discussed are also applicable to the output of any similar proteomics raw data processing software, including MaxQuant, among others.

Here we have outlined the differences to be aware of when following this course using MaxQuant output text files. The code as written will require some minor modifications to work properly with MaxQuant formatted data.

  1. The rough equivalent of the PSMs.txt file output by Proteome Discoverer is the evidence.txt file output by MaxQuant.

  2. Decoy PSMs (known false discoveries which are used to calculate false discovery rate) are automatically filtered out by Proteome Discoverer, but this is not the case with MaxQuant. Hence when working with MaxQuant outputs it is important to filter out rows with ‘+’ in the Reverse column.

  3. Equivalent column names and the type of data contained are described below. Ellipses are put where no equivalent column exists.

Naming of column headers in third party softwares

Column names are not only different between different softwares but also between different versions of the same software. Always check the column names and that they correspond to what you expect.

PSM or peptide level files

Proteome Discoverer (PSMs.txt) MaxQuant (evidence.txt)
Abundance (float) Reporter.intensity.corrected (integer)
Sequence (string) Sequence (string)
Master.Protein.Accessions (string) Leading.proteins (string)
Contaminants (string, True or False) Potential.contaminant (string, + or blank)
… Reverse (string, + or blank)
Rank (integer) …
Search.Engine.Rank (integer) …
PSM.Ambiguity (string) …
Number.of.Protein.Groups (integer) … (you might calculate this by counting the number of ; in the Leading.proteins column and adding 1)
Average.Reporter.SN (float) … (you might calculate the average reporter ion intensity and threshold based on that instead)
Isolation.Interference.in.Percent (float) PIF (float, to get the data in exactly the same format you have to calculate (1 - PIF)*100)
SPS.Mass.Matches.in.Percent (integer) …


Protein level files

Proteome Discoverer (Proteins.txt) MaxQuant (proteinGroups.txt)
Accession (string) Majority.protein.IDs (string)
Protein.FDR.Confidence.Combined (string; High, Medium, or Low) Q.value (float, a Proteome Discoverer protein FDR of ‘High’ is equivalent to a Q.value < 0.01)