The bacterial proteogenomic pipeline

PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations

(2014) A. Tovchigrechko et al.   BIOINFORMATICS

Peppy: Proteogenomic Search Software

(2013) Brian A. Risk et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomic Analysis ofBradyrhizobium japonicumUSDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline

(2013) Dhirendra Kumar et al.   MOLECULAR & CELLULAR PROTEOMICS

Rhizobial Adaptation to Hosts, a New Facet in the Legume Root-Nodule Symbiosis

(2010) Marion Koch et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

(2010) Danny A. Bitton et al.   PLoS One

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH