title: Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.
abstract: BACKGROUND
  Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise owing to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level, which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions.
  
  
  RESULTS
  We introduce Pipasic (peptide intensity-weighted proteome abundance similarity correction) as a tool that corrects identification and spectral counting-based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor, as demonstrated on examples of viral diagnostics and an acid mine drainage dataset.
  
  
  METHODS
  Pipasic source code is freely available from https://sourceforge.net/projects/pipasic/.
  
  
  BACKGROUND
  RenardB@rki.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Anke
authors.initials: A
authors.lastname: Penzlin
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Martin S
authors.initials: MS
authors.lastname: Lindner
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, GermanyResearch Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Joerg
authors.initials: J
authors.lastname: Doellinger
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, GermanyResearch Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Piotr Wojtek
authors.initials: PW
authors.lastname: Dabrowski
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Nitsche
authors.affiliation: Research Group Bioinformatics (NG4), Centre for Biological Threats and Special Pathogens 1 (ZBS 1), Centre for Biological Threats and Special Pathogens 6 (ZBS 6) and Central Administration 4 (IT), Robert Koch Institute, 13353 Berlin, Germany.
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism; D015608:Cowpox virus / Q000145:classification; D004783:Environmental Microbiology; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D001426:Bacterial Proteins; D010455:Peptides; D020543:Proteome