Hexapeptide Libraries for Enhanced Protein PTM Identification and Relative Abundance Profiling in Whole Human Saliva

被引:39
作者
Bandhakavi, Sricharan
Van Riper, Susan K. [2 ]
Tawfik, Pierre N.
Stone, Matthew D.
Haddad, Tufia [3 ]
Rhodus, Nelson L. [4 ]
Carlis, John V. [5 ]
Griffin, Timothy J. [1 ]
机构
[1] Univ Minnesota, Ctr Mass Spectrometry & Prote, Dept Biochem Mol Biol & Biophys, Minneapolis, MN 55455 USA
[2] Univ Minnesota, Dept Biomed Informat & Computat Biol, Rochester, MN 55904 USA
[3] Univ Minnesota, Masonic Canc Ctr, Minneapolis, MN 55455 USA
[4] Univ Minnesota, Dept Oral Med Diag & Radiol, Minneapolis, MN 55455 USA
[5] Univ Minnesota, Dept Comp Sci & Engn, Minneapolis, MN 55455 USA
关键词
dynamic range compression proteomics; saliva; N-linked glycoproteins; breast cancer; proteominer; PEPTIDE LIGAND LIBRARIES; N-LINKED GLYCOPROTEINS; MASS-SPECTROMETRY; BREAST-CANCER; PROTEOMICS; CAPTURE; PROTEOMINER(TM); QUANTIFICATION; GLYCOPEPTIDES; GLYCOSYLATION;
D O I
10.1021/pr100857t
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC's potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing question one, we coupled DRC with covalent glycopeptide enrichment and MS/MS. With DRC we identified similar to 2 times more N-linked glycoproteins and their glycosylation sites than without DRC, dramatically increasing the known salivary glycoprotein catalog. Addressing question two, we compared differentially stable isotope-labeled saliva samples pooled from healthy and metastatic breast cancer women using a multidimensional peptide fractionation-based work-flow, analyzing in parallel one sample portion with DRC and one portion without. Our workflow categorizes proteins with higher absolute abundance, whose relative abundance ratios are altered by DRC, from proteins of lower absolute abundance detected only after DRC. Within each of these salivary protein categories, we identified novel abundance changes putatively associated with breast cancer, demonstrating feasibility and benefits of DRC for relative abundance profiling. Collectively, our results bring us closer to realizing the full potential of DRC for proteomic studies.
引用
收藏
页码:1052 / 1061
页数:10
相关论文
共 46 条
  • [41] Solid-phase extraction of N-linked glycopeptides
    Tian, Yuan
    Zhou, Yong
    Elliott, Sarah
    Aebersold, Ruedi
    Zhang, Hui
    [J]. NATURE PROTOCOLS, 2007, 2 (02) : 334 - 339
  • [42] Salivary diagnostics powered by nanotechnologies, proteomics and genomics
    Wong, DT
    [J]. JOURNAL OF THE AMERICAN DENTAL ASSOCIATION, 2006, 137 (03) : 313 - 321
  • [43] Systematic comparison of the human saliva and plasma proteomes
    Yan, Weihong
    Apweiler, Rolf
    Balgley, Brian M.
    Boontheung, Pinmanee
    Bundy, Jonathan L.
    Cargile, Benjamin J.
    Cole, Steve
    Fang, Xueping
    Gonzalez-Begne, Mireya
    Griffin, Timothy J.
    Hagen, Fred
    Hu, Shen
    Wolinsky, Lawrence E.
    Lee, Cheng S.
    Malamud, Daniel
    Melvin, James E.
    Menon, Rajasree
    Mueller, Michael
    Oiao, Renli
    Rhodus, Nelson L.
    Sevinsky, Joel R.
    States, David
    Stephenson, James L., Jr.
    Than, Shawn
    Yates, John R., III
    Yu, Weixia
    Xie, Hongwei
    Xie, Yongming
    Omenn, Gilbert S.
    Loo, Joseph A.
    Wong, David T.
    [J]. PROTEOMICS CLINICAL APPLICATIONS, 2009, 3 (01) : 116 - 134
  • [44] Mammaglobin: a candidate diagnostic marker for breast cancer
    Zehentner, BK
    Carter, D
    [J]. CLINICAL BIOCHEMISTRY, 2004, 37 (04) : 249 - 257
  • [45] Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    Zhang, H
    Li, XJ
    Martin, DB
    Aebersold, R
    [J]. NATURE BIOTECHNOLOGY, 2003, 21 (06) : 660 - 666
  • [46] Isolation of N-linked glycopeptides from plasma
    Zhou, Yong
    Aebersold, Ruedi
    Zhang, Hui
    [J]. ANALYTICAL CHEMISTRY, 2007, 79 (15) : 5826 - 5837