MaxQuant comes with a brand-new search engine

J Proteome Res. 2011 Jan 21. [Epub ahead of print]

Andromeda - a peptide search engine integrated into the MaxQuant environment.

Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M.

Abstract

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify co-fragmented peptides, significantly improving the total number of identified peptides.

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.