title: Tools for exploring the proteomosphere.
abstract: Homology-driven proteomics aims at exploring the proteomes of organisms with unsequenced genomes that, despite rapid genomic sequencing progress, still represent the overwhelming majority of species in the biosphere. Methodologies have been developed to enable automated LC-MS/MS identifications of unknown proteins, which rely on the sequence similarity between the fragmented peptides and reference database sequences from phylogenetically related species. However, because full sequences of matched proteins are not available and matching specificity is reduced, estimating protein abundances should become the obligatory element of homology-driven proteomics pipelines to circumvent the interpretation bias towards proteins from evolutionary conserved families.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany. shevchenko@mpi-cbg.de
authors.forename: Andrej
authors.initials: A
authors.lastname: Shevchenko
authors.forename: Cristina-Maria
authors.initials: CM
authors.lastname: Valcu
authors.forename: Magno
authors.initials: M
authors.lastname: Junqueira
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002853:Chromatography, Liquid / Q000379:methods*; D003201:Computers; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; D020543:Proteome