title: Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry.
abstract: BACKGROUND
  Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency.
  
  
  RESULTS
  We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties.
  
  
  CONCLUSIONS
  For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.
authors.affiliation: University of Tübingen, Center for Bioinformatics, Sand 1, D-72076 Tübingen, Germany. hannes.planatscher@uni-tuebingen.de.
authors.forename: Hannes
authors.initials: H
authors.lastname: Planatscher
authors.forename: Jochen
authors.initials: J
authors.lastname: Supper
authors.forename: Oliver
authors.initials: O
authors.lastname: Poetz
authors.forename: Dieter
authors.initials: D
authors.lastname: Stoll
authors.forename: Thomas
authors.initials: T
authors.lastname: Joos
authors.forename: Markus F
authors.initials: MF
authors.lastname: Templin
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell