title: Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants.
abstract: Protein turnover is an important aspect of the regulation of cellular processes for organisms when responding to developmental or environmental cues. The measurement of protein turnover in plants, in contrast to that of rapidly growing unicellular organismal cultures, is made more complicated by the high degree of amino acid recycling, resulting in significant transient isotope incorporation distributions that must be dealt with computationally for high throughput analysis to be practical. An algorithm in R, ProteinTurnover, was developed to calculate protein turnover with transient stable isotope incorporation distributions in a high throughput automated manner using high resolution MS and MS/MS proteomic analysis of stable isotopically labeled plant material. ProteinTurnover extracts isotopic distribution information from raw MS data for peptides identified by MS/MS from data sets of either isotopic label dilution or incorporation experiments. Variable isotopic incorporation distributions were modeled using binomial and beta-binomial distributions to deconvolute the natural abundance, newly synthesized/partial-labeled, and fully labeled peptide distributions. Maximum likelihood estimation was performed to calculate the distribution abundance proportion of old and newly synthesized peptides. The half-life or turnover rate of each peptide was calculated from changes in the distribution abundance proportions using nonlinear regression. We applied ProteinTurnover to obtain half-lives of proteins from enriched soluble and membrane fractions from Arabidopsis roots.
authors.affiliation: Department of Horticultural Science, University of Minnesota , Twin Cities, Minnesota 55108, United States.|Department of Plant Biology, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: Kai-Ting
authors.initials: KT
authors.lastname: Fan
authors.affiliation: School of Statistics, University of Minnesota , Twin Cities, Minnesota 55108, United States.
authors.forename: Aaron K
authors.initials: AK
authors.lastname: Rendahl
authors.affiliation: Department of Horticultural Science, University of Minnesota , Twin Cities, Minnesota 55108, United States.|Microbial and Plant Genomics Institute, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: Wen-Ping
authors.initials: WP
authors.lastname: Chen
authors.affiliation: Department of Horticultural Science, University of Minnesota , Twin Cities, Minnesota 55108, United States.|Microbial and Plant Genomics Institute, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: Dana M
authors.initials: DM
authors.lastname: Freund
authors.affiliation: Microbial and Plant Genomics Institute, University of Minnesota , Twin Cities, Minnesota 55455, United States.|Department of Plant Biology, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: William M
authors.initials: WM
authors.lastname: Gray
authors.affiliation: Department of Horticultural Science, University of Minnesota , Twin Cities, Minnesota 55108, United States.|Microbial and Plant Genomics Institute, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: Jerry D
authors.initials: JD
authors.lastname: Cohen
authors.affiliation: Department of Horticultural Science, University of Minnesota , Twin Cities, Minnesota 55108, United States.|Microbial and Plant Genomics Institute, University of Minnesota , Twin Cities, Minnesota 55455, United States.|Department of Plant Biology, University of Minnesota , Twin Cities, Minnesota 55455, United States.
authors.forename: Adrian D
authors.initials: AD
authors.lastname: Hegeman
mesh_terms: D000465:Algorithms; D006207:Half-Life; D007553:Isotope Labeling; D016013:Likelihood Functions; D010940:Plant Proteins / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D053719:Tandem Mass Spectrometry
chemical_list: D010940:Plant Proteins; D020543:Proteome
keywords: Arabidopsis thaliana; metabolic labeling; protein turnover rates; proteome dynamics; stable isotope
references.citation: J Proteome Res. 2004 Sep-Oct;3(5):958-64
references.pmid: 15473683
references.citation: Nat Biotechnol. 2012 Oct;30(10):918-20
references.pmid: 23051804
references.citation: J Biol Chem. 1980 May 10;255(9):4125-30
references.pmid: 6989832
references.citation: Eur J Pediatr. 1997 Aug;156 Suppl 1:S12-7
references.pmid: 9266209
references.citation: Anal Chem. 2003 Dec 15;75(24):6912-21
references.pmid: 14670053
references.citation: Anal Chem. 2011 Mar 1;83(5):1665-72
references.pmid: 21314131
references.citation: Proteome Sci. 2011 Feb 10;9(1):9
references.pmid: 21310072
references.citation: Genome Biol. 2010;11(8):R86
references.pmid: 20738864
references.citation: Nat Rev Genet. 2012 Mar 13;13(4):227-32
references.pmid: 22411467
references.citation: Expert Rev Proteomics. 2006 Feb;3(1):97-110
references.pmid: 16445354
references.citation: Plant J. 2010 Aug;63(4):680-95
references.pmid: 20525007
references.citation: Anal Chem. 1996 Mar 1;68(5):850-8
references.pmid: 8779443
references.citation: J Am Soc Mass Spectrom. 2005 Jul;16(7):1181-91
references.pmid: 15922621
references.citation: J Biol Chem. 1980 Mar 25;255(6):2524-32
references.pmid: 6987224
references.citation: Rapid Commun Mass Spectrom. 2013 Jan 15;27(1):157-62
references.pmid: 23239329
references.citation: Mol Cell Proteomics. 2011 Dec;10(12):M111.010728
references.pmid: 21937731
references.citation: J Cell Biol. 1964 Oct;23:188-93
references.pmid: 14228511
references.citation: BMC Genomics. 2009 Oct 31;10:505
references.pmid: 19878582
references.citation: Nature. 1959 Aug 29;184(Suppl 10):729-30
references.pmid: 13812799
references.citation: Mol Cell Proteomics. 2005 Jul;4(7):857-72
references.pmid: 15849272
references.citation: Proteomics. 2009 Jan;9(1):205-9
references.pmid: 19053139
references.citation: Plant Cell. 2013 Feb;25(2):694-714
references.pmid: 23444331
references.citation: J Proteome Res. 2012 Jan 1;11(1):476-86
references.pmid: 22077659
references.citation: FASEB J. 2003 Aug;17(11):1470-86
references.pmid: 12890701
references.citation: Nature. 2011 May 19;473(7347):337-42
references.pmid: 21593866
references.citation: Plant Physiol. 1997 Oct;115(2):317-9
references.pmid: 9342857
references.citation: Mol Cell Proteomics. 2012 Jun;11(6):M111.010025
references.pmid: 22215636
references.citation: Anal Chem. 2008 Jan 15;80(2):396-406
references.pmid: 18085750
references.citation: Anal Chem. 2004 Jan 1;76(1):86-97
references.pmid: 14697036
references.citation: PLoS One. 2014 Apr 15;9(4):e94692
references.pmid: 24736476
references.citation: Anal Chem. 1996 Jul 1;68(13):2027-30
references.pmid: 21619291
references.citation: Science. 2012 Feb 24;335(6071):942
references.pmid: 22300851
references.citation: Proteomics. 2010 Mar;10(6):1265-9
references.pmid: 20077414
references.citation: Proteomics. 2007 Apr;7(8):1279-92
references.pmid: 17443642
references.citation: Clin Sci (Lond). 1991 Apr;80(4):277-80
references.pmid: 1851061
references.citation: Mol Cell Proteomics. 2007 May;6(5):860-81
references.pmid: 17293592
references.citation: Biochem J. 1993 Sep 1;294 ( Pt 2):427-33
references.pmid: 8373357
references.citation: Plant J. 2014 May;78(3):424-40
references.pmid: 24547885
references.citation: Nat Struct Mol Biol. 2011 May;18(5):520-8
references.pmid: 21540891
references.citation: Genome Res. 2005 Oct;15(10):1451-5
references.pmid: 16169926
references.citation: Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14508-13
references.pmid: 20699386
references.citation: Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21
references.pmid: 20069535
references.citation: Proteome Sci. 2014 Mar 03;12(1):14
references.pmid: 24580857
references.citation: Mol Cell Proteomics. 2002 Aug;1(8):579-91
references.pmid: 12376573
references.citation: Mol Cell Biol. 1999 Mar;19(3):1720-30
references.pmid: 10022859
references.citation: FASEB J. 2001 Jul;15(9):1562-8
references.pmid: 11427488
references.citation: Trends Biotechnol. 2012 Dec;30(12):668-76
references.pmid: 23107010
references.citation: Anal Chem. 2012 May 1;84(9):4014-21
references.pmid: 22444387
references.citation: Trends Cell Biol. 2011 May;21(5):293-303
references.pmid: 21474317
references.citation: Plant Physiol. 2015 May;168(1):74-93
references.pmid: 25810096