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I propose to write a module to process MaxQuant results files.
MaxQuant is a program written by Jurgen Cox in the Mann lab, a big
proteomics lab in the Max Planck Institute.  It takes the data output
from an Orbitrap and gets it ready for Mascot
( ), and then takes the output from both and
combines them to give results.  It's strengths are in processing large
datasets, filtering based on false positives, label-free quantitation
and especially SILAC.

I am always processing the files output by MaxQuant, but find myself
re-writing code, so I thought I might as well write a module and then
others can use it too.

The data output by maxquant is contained in several text files, which
basically look like the tables of a relational database.  One file has
peptides, with protein IDs of the proteins those peptides come from,
and there's a proteins table, with the corresponding peptide IDs,
there are evidence and msms files, and more.  The files are REALLY BIG
and so manual operations are mostly impossible.  Manipulation with
perl is easy :-)

I suggest that the module has both object oriented and procedural
interfaces and that it should probably use the functionality from
another table-parsing module, such as Parse::CSV.  The different
tables may or may not be represented by the same object, since most of
the functionality required is the same for each table (getting related
rows from another table, selecting rows based on values/ranges, etc).

Does anybody have any comments?

Re: Bio::MaxQuant

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MaxQuant has released a tool called Viewer,  maybe you cant try it~

I am more interested that if there are modules for parse mass data

Bioperl is very powerful module but lacks of tools for mass spectrum.

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