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muxQuant is copyright (c) 2007 Magnus Palmblad

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This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License.

About muxQuant

muxQuant is a tool for multiplexed relative quantitation of peptides and proteins in quantitative proteomics, originally described in Palmblad et al. Journal of Proteome Research, 7(2), 780-785 (2008). From accurate mass LC-MS data in mzXML aligned with peptide identifications based on MS/MS in pepXML (see msalign), muxQuant extracts isotopic envelopes for all identified peptides and fits calculated envelopes by weighing the isotopic distributions for each level of stable isotope and peptide. The individual isotopic distributions are calculated efficiently using the same code and FFTW library used by AUTOHD

muxQuant also uses the Random Access Minimal Parser (RAMP) library to read data in mzXML.

Multiplexed relative quantitation by muxQuant

Download muxQuant here. (Right-click and choose "Save Link As...".)

Compiling muxQuant

Compile muxQuant with: gcc -o muxQuant base64.c ramp.c muxQuant.c -I. -lm -lz -lfftw3 -lgsl

Using muxQuant

Usage: muxQuant -C<12|13> -N<14|15> -p<MS/MS pepXML filename> -m<MS dataset in mzXML> -a<alignment function> -f<fraction C-13 or N-15 filename> -e<max. mass difference between MS and MS/MS datasets (in ppm)> -I<integration window (in ppm)> [-i<ion score cutoff> -b<background mean>,<background standard deviation> -R<MS begin scan>,<MS end scan> -o<output quantitation file> -maximum -nographics]

where the

-C or -N flag is followed by the isotope(s) used for peptide identification

<MS/MS pepXML filename> is the peptide identifications results from the LC-MS/MS dataset in pepXML format (example)

<MS dataset in mzXML> the (accurate) LC-MS data in mzXML (either line or full profile spectra)

<alignment function> is the resulting alignment (piecewise linear function) from msalign (example)

<fraction C-13 or N-15 filename> is the name of the file containing the different levels of stable isotope(s) in the differentially labeled samples (example)

<integration window (in ppm)> is the window around each isotopic peak to be integrated (or search for maximum) in the mzXML MS data

<output quantitation file> is the name of the file to which the quantitation results will be written (with different filename extension)

and the -maximum flag tells muxQuant to use maximum peak intensities rather than integrating the area (recommended for line spectra mzXML, especially from FTICR)

optionally, muxQuant can be run in a "list mode" using -L and suppling a list of identified peptides and isotopic envelopes (example)