In our proteomics platform, we need to analyse LC-MS data:
- in a versatile way (we had different kind of experiment scenarios to treat),
- in a secure and traceable way (this is research data so we have to be able to precisely follow, explain and reproduce every single step),
- in a hardware/software independent way (we do not have big computing servers or unlimited money to buy Windows licences every year, we have simple personal computer, but robust as most of the time they run under Linux ),
- if it is possible, we want to process large amounts of data in an automatic fast and light way.
But, we are not a software editor platform, so we first tried every existing quantification tool. But no one fitted our expectations. They were either limited in analysis types, were often obscure in their analysis, and very often they were specific to Windows systems or graphical interfaces. That is when we began developing our own pipelines and tools, which we kept private and used for our own need. But overtime, our tools became more complete and less specific to our platform needs. That is why, three years after, we decided to publicly release MassChroQ as a free, open source software.
MassChroQ is very flexible because it is fully configurable, the user can adapt the various parameters to its data quality, to its spectrometer type and to its biological interests (one can perform with or without labelling quantification, complex peptide/protein separation (2D-LC) etc.).
MassChroQ produces precise traces of all the analysis steps it performs (of the alignments, of XIC-s with and without signal filtering, of the peaks detected on them, of the matched peaks, etc.). These traces are in practice very useful, not only do they guide the user through the parameter adjustment process, but once these parameters adjusted and the analysis is over, they can be themselves used for statistical analysis, plots, etc.
It can automatically handle hard workloads of LC-MS data, fastly (takes less than three minutes for a full analysis of 1Go of profile mzXML data) and lightly (it uses at most 450 Mo of RAM, your personal computer stays fully functional).
Last but not least, MassChroQ is a free open-source software that comes with a library which can easily be integrated into your own pipeline. It is made available for Windows and Linux systems, and your are free to compile it on other systems. Every data that it uses or produces are in open standard formats (mzXML, mzML, gnumeric, tsv, ods).