MassWiz

MassWiz is an open source software for protein identification from mass spectrometry data. It is developed and maintained at Institute of Genomics and Integrative Biology. It was developed to better the existing methods by finding semi and non-enzymatic peptides to enhance the confidence in protein identifications. The Software aims at easy usability by automating the downstream analysis by integrating significance assessment by integrating FDR analysis which uses a target-decoy database search approach.
Features
MassWiz has a Windows 32 command line version for high throughput data analyses. The FDR analysis is directly plugged into the algorithm and the users can choose the type of target-decoy strategy they want to follow (i.e. either concatenated or separate target-decoy search).
It has been shown that MassWiz performs better than commonly used search algorithms and identifies highest number of consensus peptides which are of high confidence.<ref name="YadavKumar2011" /> Because of the comprehensive comparison of Spectra(PSMs-peptide spectrum matches) and peptides across various MS platforms with four other algorithms - Mascot, OMSSA, X!Tandem and Sequest, the MassWiz benchmarks can be used for deciding on choice of algorithms in analysis pipelines.
Webserver Algorithms and Tools
#Probability and intensity based PMF search
#Intensity and ion abundance based MS/MS search identifying semi+non-enzymatic peptides
#Candidate peptide validation
#Mass and pI calculator
#mzXML file converter
#Custom Database for targeted studies
#Customized local BLAST in the custom database
#Graphical representation of the matches found.

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