title: Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
abstract: A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.
authors.affiliation: National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Rudnick
authors.forename: Karl R
authors.initials: KR
authors.lastname: Clauser
authors.forename: Lisa E
authors.initials: LE
authors.lastname: Kilpatrick
authors.forename: Dmitrii V
authors.initials: DV
authors.lastname: Tchekhovskoi
authors.forename: Pedatsur
authors.initials: P
authors.lastname: Neta
authors.forename: Niksa
authors.initials: N
authors.lastname: Blonder
authors.forename: Dean D
authors.initials: DD
authors.lastname: Billheimer
authors.forename: Ronald K
authors.initials: RK
authors.lastname: Blackman
authors.forename: David M
authors.initials: DM
authors.lastname: Bunk
authors.forename: Helene L
authors.initials: HL
authors.lastname: Cardasis
authors.forename: Amy-Joan L
authors.initials: AJ
authors.lastname: Ham
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Jaffe
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Kinsinger
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mesri
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Neubert
authors.forename: Birgit
authors.initials: B
authors.lastname: Schilling
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.forename: Tony J
authors.initials: TJ
authors.lastname: Tegeler
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Vega-Montoto
authors.forename: Asokan Mulayath
authors.initials: AM
authors.lastname: Variyath
authors.forename: Mu
authors.initials: M
authors.lastname: Wang
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Whiteaker
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Fisher
authors.forename: Bradford W
authors.initials: BW
authors.lastname: Gibson
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Paulovich
authors.forename: Fred E
authors.initials: FE
authors.lastname: Regnier
authors.forename: Henry
authors.initials: H
authors.lastname: Rodriguez
authors.forename: Cliff
authors.initials: C
authors.lastname: Spiegelman
authors.forename: Paul
authors.initials: P
authors.lastname: Tempst
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Stein
mesh_terms: D000818:Animals; D002645:Chickens; D002853:Chromatography, Liquid / Q000379:methods* / Q000592:standards*; D004527:Egg Proteins / Q000032:analysis; D007753:Laboratories; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods* / Q000592:standards*
chemical_list: D004527:Egg Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins