MMSAT: Metabolite Mass Spectrometry Analysis Tool

In LC-MS/MS and GC-MS/MS experiments a combination of precursor and product masses, together with the column elution time, is used to identify and characterise the metabolites within a sample with a high degree of accuracy. Metabolite profiling experiments that use either scanning over a defined mass range (i.e. precursor ion scanning) or a list of defined precursor and product ion pairs (i.e. selected reaction monitoring, SRM) often yield hundreds of distinct peaks that may be of interest. We describe MMSAT (Metabolite Mass Spectrometry Analysis Tool) which is able to align peaks from SRM-based experiments across multiple samples, allowing the user to compare the abundance of multiple different metabolites across multiple samples. The output is an tab delimited table that can be further analysed in popular tool such as Excel or R.

Below is the web interface for accessing MMSAT. The software accepts any LC-MS/MS data in mzXML format (currently only tested with raw data acquired on the ThermoFinnigan TSQ, ABI QStar and Waters Micromass QToF). A batch coversion script using ReAdW can be downloaded here:

The source code is available for download: MMSAT_1.1.tgz (for to non-commercial users only).

Details regarding the algorithm and implementation of MMSAT is described in:

Wong JWH, Abuhusain HJ, McDonald KL, Don AS (2011) MMSAT: Automated Quantification of Metabolites in Selected Reaction Monitoring Experiments. Anal Chem. 84 (1), 470–474

It you cannot see the interface for MMSAT below, right click on the area below click here.

The webserver will output all results in a zipped file. This zip file contains:

  • Inputfile_xxx_compiled.txt - This file contains the summarised aligned data
  • Inputfile_xxx_diff.txt - This file contains shifted retention times for all samples required for final alignment
  • *.out - Raw output from MMSAT of each input file. Contains information for quality control such as peak start/end, etc.