GenoSuite

GenoSuite is an automated pipeline for proteogenomic analysis from mass spectrometry proteomics data using four open source peptide identification algorithms. By applying proteomic search by multiple algorithms, GenoSuite provides better coverage of proteome at fixed FDR. It automatically classifies identified peptides into categories of already annotated genes or originating from an genomic region, unknown for translation. GenoSuite can be used for genome annotation/re-annotation projects provided tandem mass spectrometry data and genome sequence are available. Search parameters can be customized and and any combination of algorithm can be chosen for search. The four algorithms configured are OMSSA, X!Tandem, InsPecT and MassWiz.

New version GenoSuite_v_2.0.3 released. This new version allows to add a contaminant protein list to the genome translated search database. Bugs related to PSM XML generation and visualization are also fixed.

GenoSuite2 is an updated version where following major changes are made to make is more applicable and accurate.

(1) Combined FDRScore based strategy has been implemented to integrate results from four algorithms at the level of peptide spectrum matches(PSMs). This approach was originally proposed and implemented on OMSSA, Mascot and X!Tandem by Jones AR et al.(Proteomics 2009). In GenoSuite we have extended this approach to InsPecT and MassWiz. This allows us to estimate and control false discovery rates after the integration of results from different algorithms.

(2) To insure low protein level FDR, it automatically reports proteins identified with 2 or more peptides or in case of single peptide identifiecations should have 5 or more significant PSMs.

(3) ORF_mapper utility of GenoSuite2 now takes gene prediction input in more generic GFF format.

We applied GenoSuite on publically available proteomics datasets and re-annotated follwoing bacteria.
Bradyrhizobium japonicum USDA110

https://sourceforge.net/p/proteogenomic/wiki/Proteogenomic%20re-annotation%20of%20Bradyrhizobium%20japonicum/

Shigella flexneri 2a str. 2457T

https://sourceforge.net/p/proteogenomic/wiki/Proteogenomic%20Re-annotation%20of%20Shigellla%20flexneri/

Methylobacterium extorquens AM1

https://sourceforge.net/p/proteogenomic/wiki/Methylobacterium%20extorquens%20AM1/

Citing GenoSuite

If GenoSuite is helpful to your research, please consider citing following reference.

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline. Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Mol Cell Proteomics. 2013 Jul 23.

[Dhirendra Kumar]

GenoSuite is a framework developed for proteogenomic analysis. Currently it supports prokaryotic proteogenomic analysis. Prokaryotic Proteogenomic Tool(PPT) is developed as a part of GenoSuite framework. PPT is for finding novel translations in prokaryotic genomes and is dependent on Mass Spectrometry based proteomics data and related genome sequence.

Some Key features of the tool are....
(1) Configured for 4 open source algorithms to perform database searching for peptide identification. Any combination of the 4 algorithm can be chosen. Number of algorithms identifying a peptide can be used as a quality measure for peptide assignment.
(2) Lists out the genome search specific peptides(Novel peptides).
(3) Spectral matches can be visualized for the quality assessment.
(4) Lists out the novel proteins and changes in the existing protein annotations.
(5) A Visual genomic context of the novel peptides can also be generated.