MaxQuant

"MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (e.g. Orbitrap and FT) data. It can be used for protein identification for non-labeled samples and identification and quantification for SILAC-labeled samples. MaxQuant includes all steps needed in a computational proteomic platform except that it uses the Mascot search algorithm for peptide identification. In brief, raw data acquired on Orbitrap, is processed using MaxQuant’s Quant module". The processed data is further searched with Mascot. Nature Protocols feature a step-by-step tutorial on how to configure and use this powerful software. http://www.natureprotocols.com/2009/04/16/a_practical_guide_to_the_maxqu.php


The program runs pretty slow on PC if the MS dataset is large. Some procedures appear awkward. For instance, if you change  the fasta files, the Quant step must be conducted completely, taking a lot of time away. Also not every lab has access to Mascot search engine. A relieve news is that the up to coming release of MaxQuant will  have its own search engine. 


It is designed for SILAC labeling MS data. Though it can be forced to analyze unlabelled data, but the results are generally poor.


The MSQuan is also a sibling software from MaxQuant, from the same core developers. Unfortunately, it is not fully maintained, and much harder to use,  according to my personal experience.