title: Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.
abstract: BACKGROUND
  For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays.
  
  
  BACKGROUND
  The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.
authors.affiliation: University of Washington, Seattle, WA; ahoof@u.washington.edu apaulovi@fhcrc.org.
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Hoofnagle
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA;
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Whiteaker
authors.affiliation: Broad Institute, Cambridge, MA;
authors.forename: Steven A
authors.initials: SA
authors.lastname: Carr
authors.affiliation: Broad Institute, Cambridge, MA;
authors.forename: Eric
authors.initials: E
authors.lastname: Kuhn
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: New England Peptide, Inc., Gardner, MA;
authors.forename: Sam A
authors.initials: SA
authors.lastname: Massoni
authors.affiliation: Johns Hopkins University, Baltimore, MD;
authors.forename: Stefani N
authors.initials: SN
authors.lastname: Thomas
authors.affiliation: Washington University, St Louis, MO;
authors.forename: R Reid
authors.initials: RR
authors.lastname: Townsend
authors.affiliation: Vanderbilt University, Nashville, TN;
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.affiliation: National Cancer Institute, Bethesda, MD;
authors.forename: Emily
authors.initials: E
authors.lastname: Boja
authors.affiliation: Johns Hopkins University, Baltimore, MD;
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.affiliation: Washington University, St Louis, MO;
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Crimmins
authors.affiliation: Washington University, St Louis, MO;
authors.forename: Sherri R
authors.initials: SR
authors.lastname: Davies
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Yuqian
authors.initials: Y
authors.lastname: Gao
authors.affiliation: National Cancer Institute, Bethesda, MD;
authors.forename: Tara R
authors.initials: TR
authors.lastname: Hiltke
authors.affiliation: ESAC, Inc., Rockville, MD;
authors.forename: Karen A
authors.initials: KA
authors.lastname: Ketchum
authors.affiliation: National Cancer Institute, Bethesda, MD;
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Kinsinger
authors.affiliation: National Cancer Institute, Bethesda, MD;
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mesri
authors.affiliation: Washington University, St Louis, MO;
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Meyer
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Wei-Jun
authors.initials: WJ
authors.lastname: Qian
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA;
authors.forename: Regine M
authors.initials: RM
authors.lastname: Schoenherr
authors.affiliation: Washington University, St Louis, MO;
authors.forename: Mitchell G
authors.initials: MG
authors.lastname: Scott
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Tujin
authors.initials: T
authors.lastname: Shi
authors.affiliation: Frederick National Laboratory for Cancer Research, Frederick, MD;
authors.forename: Gordon R
authors.initials: GR
authors.lastname: Whiteley
authors.affiliation: University of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: John A
authors.initials: JA
authors.lastname: Wrobel
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Chaochao
authors.initials: C
authors.lastname: Wu
authors.affiliation: Eli Lilly and Company, Indianapolis, IN;
authors.forename: Brad L
authors.initials: BL
authors.lastname: Ackermann
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland;
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Mayo Clinic College of Medicine, Rochester, MN;
authors.forename: David R
authors.initials: DR
authors.lastname: Barnidge
authors.affiliation: NIST, Gaithersburg, MD;
authors.forename: David M
authors.initials: DM
authors.lastname: Bunk
authors.affiliation: Quest Diagnostics, San Juan Capistrano, CA;
authors.forename: Nigel
authors.initials: N
authors.lastname: Clarke
authors.affiliation: 21st Century Biochemicals, Inc., Marlborough, MA;
authors.forename: Jordan B
authors.initials: JB
authors.lastname: Fishman
authors.affiliation: Laboratory Corporation of America Holdings, Inc., Burlington, NC;
authors.forename: Russ P
authors.initials: RP
authors.lastname: Grant
authors.affiliation: Institute for Systems Biology, Seattle, WA;
authors.forename: Ulrike
authors.initials: U
authors.lastname: Kusebauch
authors.affiliation: University of Utah and ARUP Laboratories, Salt Lake City, UT;
authors.forename: Mark M
authors.initials: MM
authors.lastname: Kushnir
authors.affiliation: NIST, Gaithersburg, MD;
authors.forename: Mark S
authors.initials: MS
authors.lastname: Lowenthal
authors.affiliation: Institute for Systems Biology, Seattle, WA;
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: Pfizer, Inc., Andover, MA;
authors.forename: Hendrik
authors.initials: H
authors.lastname: Neubert
authors.affiliation: Gilead Sciences, Inc., Foster City, CA;
authors.forename: Scott D
authors.initials: SD
authors.lastname: Patterson
authors.affiliation: University of Utah and ARUP Laboratories, Salt Lake City, UT;
authors.forename: Alan L
authors.initials: AL
authors.lastname: Rockwood
authors.affiliation: Thermo Fisher Scientific, Rockford, IL;
authors.forename: John
authors.initials: J
authors.lastname: Rogers
authors.affiliation: Mayo Clinic College of Medicine, Rochester, MN;
authors.forename: Ravinder J
authors.initials: RJ
authors.lastname: Singh
authors.affiliation: Cedars Sinai Medical Center, Los Angeles, CA;
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Van Eyk
authors.affiliation: Wake Forest School of Medicine, Winston-Salem, NC;
authors.forename: Steven H
authors.initials: SH
authors.lastname: Wong
authors.affiliation: Enanta Pharmaceuticals, Watertown, MA;
authors.forename: Shucha
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Johns Hopkins University, Baltimore, MD;
authors.forename: Daniel W
authors.initials: DW
authors.lastname: Chan
authors.affiliation: University of North Carolina School of Medicine, Chapel Hill, NC;
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
authors.affiliation: Baylor College of Medicine, Houston, TX.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Ellis
authors.affiliation: Vanderbilt University, Nashville, TN;
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Karin D
authors.initials: KD
authors.lastname: Rodland
authors.affiliation: National Cancer Institute, Bethesda, MD;
authors.forename: Henry
authors.initials: H
authors.lastname: Rodriguez
authors.affiliation: Pacific Northwest National Laboratory, Richland, WA;
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: Johns Hopkins University, Baltimore, MD;
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Johns Hopkins University, Baltimore, MD;
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, WA; ahoof@u.washington.edu apaulovi@fhcrc.org.
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Paulovich
mesh_terms: D019411:Clinical Laboratory Techniques; D017408:Guidelines as Topic; D006801:Humans; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis* / Q000302:isolation & purification; D040901:Proteomics; D012108:Research Personnel; D013048:Specimen Handling
chemical_list: D010455:Peptides