title: STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.
abstract: For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.
authors.affiliation: Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA99352, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Piehowski
authors.forename: Vladislav A
authors.initials: VA
authors.lastname: Petyuk
authors.forename: John D
authors.initials: JD
authors.lastname: Sandoval
authors.forename: Kristin E
authors.initials: KE
authors.lastname: Burnum
authors.forename: Gary R
authors.initials: GR
authors.lastname: Kiebel
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Monroe
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis / Q000737:chemistry; D001798:Blood Proteins / Q000032:analysis / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D010446:Peptide Fragments / Q000032:analysis / Q000737:chemistry*; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D020592:Shewanella; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D001798:Blood Proteins; D010446:Peptide Fragments; D011506:Proteins