Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.
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.
Rudnick
Paul A
PA
National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
Clauser
Karl R
KR
Kilpatrick
Lisa E
LE
Tchekhovskoi
Dmitrii V
DV
Neta
Pedatsur
P
Blonder
Niksa
N
Billheimer
Dean D
DD
Blackman
Ronald K
RK
Bunk
David M
DM
Cardasis
Helene L
HL
Ham
Amy-Joan L
AJ
Jaffe
Jacob D
JD
Kinsinger
Christopher R
CR
Mesri
Mehdi
M
Neubert
Thomas A
TA
Schilling
Birgit
B
Tabb
David L
DL
Tegeler
Tony J
TJ
Vega-Montoto
Lorenzo
L
Variyath
Asokan Mulayath
AM
Wang
Mu
M
Wang
Pei
P
Whiteaker
Jeffrey R
JR
Zimmerman
Lisa J
LJ
Carr
Steven A
SA
Fisher
Susan J
SJ
Gibson
Bradford W
BW
Paulovich
Amanda G
AG
Regnier
Fred E
FE
Rodriguez
Henry
H
Spiegelman
Cliff
C
Tempst
Paul
P
Liebler
Daniel C
DC
Stein
Stephen E
SE
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*
D004527:Egg Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins