MassWiz

MassWiz is an open source software for protein identification from mass spectrometry data.^[1] Developed at Institute of Genomics and Integrative Biology, it is currently in its beta release. It has been 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 after identification of peptides by incorporating significance estimation of peptide hits by integrating FDR analysis.

Commandline version

MassWiz has a Windows 32 command line version ( Sourceforge link [2]) 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).^[3][4]

Webserver Algorithms and Tools

1. Probability and intensity based PMF search
2. Intensity and ion abundance based MS/MS search identifying semi+non-enzymatic peptides
3. Candidate peptide validation
4. Mass and pI calculator
5. mzXML file converter
6. Custom Database for targeted studies
7. Customized local BLAST in the custom database
8. Graphical representation of the matches found.

See also

• mass spectrometry
• mass spectrometry software
• proteomics

References

1. ^ Amit K. Yadav, Dhirendra Kumar, Debasis Dash. MassWiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. Journal of Proteome Research
2. ^ Project Page at Sourceforge
3. ^ Amit K. Yadav, Dhirendra Kumar, Debasis Dash. MassWiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry. Journal of Proteome Research
4. ^ Yadav AK, Bhardwaj G, Basak T, Kumar D, Ahmad S, et al. 2011 A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery. PLoS ONE 6(9): e24442. doi:10.1371/journal.pone.0024442

External links

• MassWiz project page