title: The bacterial proteogenomic pipeline.
abstract: BACKGROUND
  Proteogenomics combines the cutting-edge methods from genomics and proteomics. While it has become cheap to sequence whole genomes, the correct annotation of protein coding regions in the genome is still tedious and error prone. Mass spectrometry on the other hand relies on good characterizations of proteins derived from the genome, but can also be used to help improving the annotation of genomes or find species specific peptides. Additionally, proteomics is widely used to find evidence for differential expression of proteins under different conditions, e.g. growth conditions for bacteria. The concept of proteogenomics is not altogether new, in-house scripts are used by different labs and some special tools for eukaryotic and human analyses are available.
  
  
  RESULTS
  The Bacterial Proteogenomic Pipeline, which is completely written in Java, alleviates the conducting of proteogenomic analyses of bacteria. From a given genome sequence, a naïve six frame translation is performed and, if desired, a decoy database generated. This database is used to identify MS/MS spectra by common peptide identification algorithms. After combination of the search results and optional flagging for different experimental conditions, the results can be browsed and further inspected. In particular, for each peptide the number of identifications for each condition and the positions in the corresponding protein sequences are shown. Intermediate and final results can be exported into GFF3 format for visualization in common genome browsers.
  
  
  CONCLUSIONS
  To facilitate proteogenomics analyses the Bacterial Proteogenomic Pipeline is a set of comprehensive tools running on common desktop computers, written in Java and thus platform independent. The pipeline allows integrating peptide identifications from various algorithms and emphasizes the visualization of spectral counts from different experimental conditions.
authors.forename: Julian
authors.initials: J
authors.lastname: Uszkoreit
authors.forename: Nicole
authors.initials: N
authors.lastname: Plohnke
authors.forename: Sascha
authors.initials: S
authors.lastname: Rexroth
authors.forename: Katrin
authors.initials: K
authors.lastname: Marcus
authors.forename: Martin
authors.initials: M
authors.lastname: Eisenacher
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020369:Bradyrhizobium / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D040901:Proteomics / Q000379:methods*; D046939:Synechocystis / Q000235:genetics*; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins