Introduction
Mass spectrometry is involved in many fields of modern biochemistry. It has become a common tool not only for precise mass measurement, but also for protein identification, peptide sequencing, the identification of various post-translational modifications, and even for the structural characterization of proteins or protein complexes. A variety of software tools exist for data analysis and interpretation, most of which are specifically connected with individual instruments.
Because mass spectrometry has primarily been used for large-scale protein identification in recent years, most manufacturer software is focused on this topic, together with the issue of automated high-throughput analysis. Despite this, in many instances mass spectrometry experiments still depend on the precise analysis of mass spectra, as well as on the researcher's experience.
It is common practise for commercial software tools to be tightly coupled to just one data format. Such software can only be used to analyze data from a specific instrument, and this causes serious problems for proteomic laboratories that use more than one instrument. This tight software-instrument relationship also causes problems for laboratories that do not possess their own instruments, and have to obtain mass spectra from other, collaborating, laboratories. Such laboratories have no opportunity to check and/or re-analyze the raw data themselves.
To provide a solution to these problems we have developed mMass, a package of many software tools for the precise analysis of mass spectra with respect to common proteomic tasks. Following figure illustrates the overall application schema. The first part of the analysis process concerns simple user manipulation of the loaded spectra, as well as peak labeling and data processing tasks, such as (re)calibration. The second part enables a previously created peaklist to be interpreted using one or more of the tools available, such as the Protein Digest Tool, Peptide Fragmentation Tool, Check Differences Tool, Compare Peaklist Tool and Mascot Search Tools.

Overall scheme of mMass structure and workflow.