IPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2012 Dec 11

PMID 23226516

Citations 8

Authors

Mathias Kuhring

Bernhard Y Renard

Affiliations

Soon will be listed here.

Abstract

Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we introduce iPiG as a tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is simplified and proteomic results can directly be compared to genomic data. iPiG is freely available from https://sourceforge.net/projects/ipig/. It is implemented in Java and can be run as a stand-alone tool with a graphical user-interface or integrated into existing workflows. Supplementary data are available at PLOS ONE online.

Citing Articles

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner C, Pirklbauer G, Bender A, Steen J, Choudhary J J Vis Exp. 2018; (135).

PMID: 29889196 PMC: 6101353. DOI: 10.3791/57633.

Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner C, Pirklbauer G, Bender A, Choudhary J Cell Syst. 2017; 5(2):152-156.e4.

PMID: 28837811 PMC: 5571441. DOI: 10.1016/j.cels.2017.07.007.

Methods, Tools and Current Perspectives in Proteogenomics.

Ruggles K, Krug K, Wang X, Clauser K, Wang J, Payne S Mol Cell Proteomics. 2017; 16(6):959-981.

PMID: 28456751 PMC: 5461547. DOI: 10.1074/mcp.MR117.000024.

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

Zhang J, Yang M, Zeng H, Ge F Mol Cell Proteomics. 2016; 15(11):3529-3539.

PMID: 27630248 PMC: 5098048. DOI: 10.1074/mcp.M116.060046.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.

Sheynkman G, Shortreed M, Cesnik A, Smith L Annu Rev Anal Chem (Palo Alto Calif). 2016; 9(1):521-45.

PMID: 27049631 PMC: 4991544. DOI: 10.1146/annurev-anchem-071015-041722.

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