Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.
Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize pre-analytical and analytical variation in comparative proteomics experiments.
Paulovich
Amanda G
AG
Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Billheimer
Dean
D
Ham
Amy-Joan L
AJ
Vega-Montoto
Lorenzo
L
Rudnick
Paul A
PA
Tabb
David L
DL
Wang
Pei
P
Blackman
Ronald K
RK
Bunk
David M
DM
Cardasis
Helene L
HL
Clauser
Karl R
KR
Kinsinger
Christopher R
CR
Schilling
Birgit
B
Tegeler
Tony J
TJ
Variyath
Asokan Mulayath
AM
Wang
Mu
M
Whiteaker
Jeffrey R
JR
Zimmerman
Lisa J
LJ
Fenyo
David
D
Carr
Steven A
SA
Fisher
Susan J
SJ
Gibson
Bradford W
BW
Mesri
Mehdi
M
Neubert
Thomas A
TA
Regnier
Fred E
FE
Rodriguez
Henry
H
Spiegelman
Cliff
C
Stein
Stephen E
SE
Tempst
Paul
P
Liebler
Daniel C
DC
D015415:Biomarkers / Q000378:metabolism; D002853:Chromatography, Liquid / Q000379:methods* / Q000592:standards*; D019411:Clinical Laboratory Techniques / Q000592:standards*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards*; D040901:Proteomics / Q000592:standards; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*
D015415:Biomarkers; D029701:Saccharomyces cerevisiae Proteins