title: Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems.
abstract: Mass spectrometry-based proteomics is a powerful analytical tool for investigating pathogens and their interactions within a host. The sensitivity of such analyses provides broad proteome characterization, but the sample-handling procedures must first be optimized to ensure compatibility with the technique and to maximize the dynamic range of detection. The decision-making process for determining optimal growth conditions, preparation methods, sample analysis methods, and data analysis techniques in our laboratory is discussed herein with consideration of the balance in sensitivity, specificity, and biomass losses during analysis of host-pathogen systems.
authors.affiliation: Pacific Northwest National Laboratory, Environmental and Molecular Sciences Laboratory, Richland, WA 99352, USA,
authors.forename: Heather M
authors.initials: HM
authors.lastname: Mottaz-Brewer
authors.forename: Angela D
authors.initials: AD
authors.lastname: Norbeck
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Manes
authors.forename: Charles
authors.initials: C
authors.lastname: Ansong
authors.forename: Liang
authors.initials: L
authors.lastname: Shi
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Rikihisa
authors.forename: Takane
authors.initials: T
authors.lastname: Kikuchi
authors.forename: Scott W
authors.initials: SW
authors.lastname: Wong
authors.forename: Ryan D
authors.initials: RD
authors.lastname: Estep
authors.forename: Fred
authors.initials: F
authors.lastname: Heffron
authors.forename: Ljiljana
authors.initials: L
authors.lastname: Pasa-Tolic
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D041081:Anaplasma phagocytophilum / Q000737:chemistry / Q000472:pathogenicity; D000818:Animals; D001709:Biotechnology; D002851:Chromatography, High Pressure Liquid; D018469:Ehrlichia chaffeensis / Q000737:chemistry / Q000472:pathogenicity; D006367:HeLa Cells; D054884:Host-Pathogen Interactions; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods / Q000706:statistics & numerical data; D008993:Monkeypox virus / Q000737:chemistry / Q000502:physiology; D020543:Proteome / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D012475:Salmonella / Q000737:chemistry / Q000472:pathogenicity; D012680:Sensitivity and Specificity; D049490:Systems Biology / Q000379:methods / Q000706:statistics & numerical data; D053719:Tandem Mass Spectrometry; D014616:Vaccinia virus / Q000737:chemistry / Q000472:pathogenicity
chemical_list: D020543:Proteome