title: The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses.
abstract: Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114.
authors.affiliation: From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; david.l.tabb@vanderbilt.edu kbennett@cemm.oeaw.ac.at maureen.bunger@gmail.com.
authors.forename: Keiryn L
authors.initials: KL
authors.lastname: Bennett
authors.affiliation: §University of Cincinnati, Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio, 45221-0025;
authors.forename: Xia
authors.initials: X
authors.lastname: Wang
authors.affiliation: ¶Cleveland HeartLab, Inc., Research and Development, Cleveland HeartLab, Inc., Cleveland, Ohio, 44103;
authors.forename: Cory E
authors.initials: CE
authors.lastname: Bystrom
authors.affiliation: ‖Vanderbilt University, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, 37232;
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Chambers
authors.affiliation: **Centers for Disease Control and Prevention, Emergency Response Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia, 30341;
authors.forename: Tracy M
authors.initials: TM
authors.lastname: Andacht
authors.affiliation: ‡‡Texas A&M University, Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, 77843;
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Dangott
authors.affiliation: §§CIC bioGUNE, Centro de Investigacion Cooperativa en Biociencias, ProteoRed-ISCIII, Bilbao, Spain;
authors.forename: Félix
authors.initials: F
authors.lastname: Elortza
authors.affiliation: ¶¶University of Massachusetts, Department of Biochemistry and Molecular Pharmacology Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts, 01545;
authors.forename: John
authors.initials: J
authors.lastname: Leszyk
authors.affiliation: ‖‖The Rockefeller University, Proteomics Resource Center, The Rockefeller University, New York, New York, 10065;
authors.forename: Henrik
authors.initials: H
authors.lastname: Molina
authors.affiliation: Institute for Systems Biology, Seattle, Washington, 98109;
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: University of California, Davis, Proteomics Core, University of California-Davis Genome Center, Davis, California, 95616;
authors.forename: Brett S
authors.initials: BS
authors.lastname: Phinney
authors.affiliation: Duke University, Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, North Carolina, 27708;
authors.forename: J Will
authors.initials: JW
authors.lastname: Thompson
authors.affiliation: Proteovations, LLC, RTP, North Carolina 27709 david.l.tabb@vanderbilt.edu kbennett@cemm.oeaw.ac.at maureen.bunger@gmail.com.
authors.forename: Maureen K
authors.initials: MK
authors.lastname: Bunger
authors.affiliation: ‖Vanderbilt University, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, 37232; david.l.tabb@vanderbilt.edu kbennett@cemm.oeaw.ac.at maureen.bunger@gmail.com.
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
mesh_terms: D000818:Animals; D002417:Cattle; D002853:Chromatography, Liquid / Q000379:methods*; D006801:Humans; D007753:Laboratories; D008137:Longitudinal Studies; D010455:Peptides / Q000302:isolation & purification*; D011506:Proteins / Q000032:analysis / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D011795:Surveys and Questionnaires; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides; D011506:Proteins