title: Quantitative measurement of phosphoproteome response to osmotic stress in arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC).
abstract: Global phosphorylation changes in plants in response to environmental stress have been relatively poorly characterized to date. Here we introduce a novel mass spectrometry-based label-free quantitation method that facilitates systematic profiling plant phosphoproteome changes with high efficiency and accuracy. This method employs synthetic peptide libraries tailored specifically as internal standards for complex phosphopeptide samples and accordingly, a local normalization algorithm, LAXIC, which calculates phosphopeptide abundance normalized locally with co-eluting library peptides. Normalization was achieved in a small time frame centered to each phosphopeptide to compensate for the diverse ion suppression effect across retention time. The label-free LAXIC method was further treated with a linear regression function to accurately measure phosphoproteome responses to osmotic stress in Arabidopsis. Among 2027 unique phosphopeptides identified and 1850 quantified phosphopeptides in Arabidopsis samples, 468 regulated phosphopeptides representing 497 phosphosites have shown significant changes. Several known and novel components in the abiotic stress pathway were identified, illustrating the capability of this method to identify critical signaling events among dynamic and complex phosphorylation. Further assessment of those regulated proteins may help shed light on phosphorylation response to osmotic stress in plants.
authors: Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.
authors: Liang
authors: L
authors: Xue
authors: Pengcheng
authors: P
authors: Wang
authors: Lianshui
authors: L
authors: Wang
authors: Emily
authors: E
authors: Renzi
authors: Predrag
authors: P
authors: Radivojac
authors: Haixu
authors: H
authors: Tang
authors: Randy
authors: R
authors: Arnold
authors: Jian-Kang
authors: JK
authors: Zhu
authors: W Andy
authors: WA
authors: Tao
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000378:metabolism*; D045744:Cell Line, Tumor; D006801:Humans; D013058:Mass Spectrometry; D009997:Osmotic Pressure / Q000502:physiology*; D019151:Peptide Library; D010748:Phosphopeptides / Q000378:metabolism*; D010766:Phosphorylation; D010940:Plant Proteins / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics / Q000379:methods*
chemical_list: D019151:Peptide Library; D010748:Phosphopeptides; D010940:Plant Proteins; D020543:Proteome
references: Plant Cell. 2010 May;22(5):1575-91
references: 20484005
references: Mol Cell Proteomics. 2009 Nov;8(11):2418-31
references: 19605366
references: Mol Cell Proteomics. 2008 Apr;7(4):661-71
references: 18039691
references: Anal Chem. 2007 Nov 15;79(22):8440-5
references: 17929902
references: J Proteomics. 2009 Apr 13;72(3):545-54
references: 19049910
references: Bioinformatics. 2003 Jan 22;19(2):185-93
references: 12538238
references: Plant J. 2000 Dec;24(5):655-65
references: 11123804
references: Nat Biotechnol. 2005 Nov;23(11):1391-8
references: 16273072
references: Plant Cell Physiol. 2008 Jun;49(6):912-24
references: 18436549
references: Plant Cell Rep. 2012 Jan;31(1):217-24
references: 21969089
references: Plant Physiol. 2009 Jun;150(2):889-903
references: 19376835
references: Nat Methods. 2011 Jul 10;8(8):655-8
references: 21743459
references: J Proteome Res. 2007 Aug;6(8):3134-42
references: 17625815
references: J Proteome Res. 2008 Apr;7(4):1675-82
references: 18327897
references: J Proteome Res. 2006 Sep;5(9):2339-47
references: 16944946
references: Methods Enzymol. 1997;289:336-92
references: 9353729
references: Science. 2007 May 25;316(5828):1160-6
references: 17525332
references: Plant Mol Biol. 2007 Jul;64(5):575-87
references: 17508130
references: Mol Cell Proteomics. 2011 Jan;10(1):M110.003079
references: 20972267
references: J Proteome Res. 2009 Aug;8(8):3808-15
references: 19537829
references: Mol Cell Proteomics. 2008 Apr;7(4):684-96
references: 18056256
references: Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15986-91
references: 20733066
references: J Plant Res. 2011 Jul;124(4):509-25
references: 21416314
references: Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21896-901
references: 21098265
references: Planta. 2010 May;231(6):1251-60
references: 20217124
references: Mol Cell Proteomics. 2011 Apr;10(4):M110.003087
references: 21209152
references: Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1488-93
references: 17242355
references: Plant Cell. 2000 Jan;12(1):165-78
references: 10634915
references: Anal Chem. 2003 Sep 15;75(18):4818-26
references: 14674459
references: Nat Biotechnol. 2008 Dec;26(12):1367-72
references: 19029910
references: Cell Mol Life Sci. 2012 Oct;69(19):3165-73
references: 22828864
references: Plant Cell. 2008 Apr;20(4):1101-17
references: 18441212
references: Mol Cell Proteomics. 2010 Oct;9(10):2162-72
references: 20562096
references: Plant J. 2012 Feb;69(3):489-500
references: 21974727
references: Plant Physiol. 2011 Jul;156(3):1464-80
references: 21571669
references: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6940-5
references: 12771378
references: Proc Natl Acad Sci U S A. 2009 May 19;106(20):8380-5
references: 19420218
references: Anal Chem. 2007 Aug 1;79(15):5651-8
references: 17580949
references: J Biol Chem. 2011 Jul 22;286(29):25443-9
references: 21632532
references: Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1717-22
references: 21220313
references: Anal Chem. 2002 Sep 15;74(18):4741-9
references: 12349978
references: Cell. 2010 Dec 23;143(7):1174-89
references: 21183079
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
references: 21045058
references: J Proteome Res. 2012 Jun 1;11(6):3467-79
references: 22559222
references: J Proteome Res. 2011 Dec 2;10(12):5354-62
references: 22073976
references: Anal Chem. 2010 Aug 1;82(15):6559-68
references: 20669997
references: Proc Natl Acad Sci U S A. 2006 May 2;103(18):7159-64
references: 16641100
references: Plant Cell. 1999 Sep;11(9):1743-54
references: 10488240
references: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9879-84
references: 15159549
references: Cell. 2006 Nov 3;127(3):635-48
references: 17081983
references: Mol Plant. 2011 Jan;4(1):83-96
references: 20978086
references: Bioinformatics. 2010 Apr 1;26(7):966-8
references: 20147306
references: J Comput Biol. 2012 Apr;19(4):337-48
references: 22414154
references: Mol Cell Proteomics. 2006 Oct;5(10):1927-41
references: 16857664
references: Anal Chem. 2007 Jun 15;79(12):4666-73
references: 17523591
references: J Proteome Res. 2007 Nov;6(11):4489-97
references: 17929957
references: Nat Chem Biol. 2005 Oct;1(5):252-62
references: 16408053
references: Plant J. 2000 Aug;23(3):319-27
references: 10929125
references: Mol Cell Proteomics. 2003 Nov;2(11):1198-204
references: 14506205
references: J Exp Bot. 2011 May;62(8):2679-89
references: 21252258
references: J Proteomics. 2013 Apr 9;81:80-90
references: 23036725
references: Plant J. 2008 Jul;55(1):104-17
references: 18363786
references: J Proteome Res. 2009 Mar;8(3):1168-82
references: 19178300
references: Cell. 2011 Sep 2;146(5):826-40
references: 21884940
references: Methods Mol Biol. 2011;696:353-67
references: 21063960
references: Mol Cell Proteomics. 2011 Aug;10(8):M111.009654
references: 21551504
references: J Biol Chem. 2004 Oct 1;279(40):41758-66
references: 15292193