MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (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. Eventually, the Mascot search output files are subjected to statistic analysis and protein grouping using the “Identify” module.
In this section tutorial we will discuss the algorithm, the recommended experimental setup, and hardware requirements. We will also include a walk-through of how to use MaxQuant.
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