New Views of Old Proteins: Clarifying the Enigmatic Proteome

被引:16
作者
Burnum-Johnson, Kristin E. [1 ]
Conrads, Thomas P. [2 ]
Drake, Richard R. [3 ]
Herr, Amy E. [4 ]
Iyengar, Ravi [5 ]
Kelly, Ryan T. [6 ]
Lundberg, Emma [7 ]
MacCoss, Michael J. [8 ]
Naba, Alexandra [9 ]
Nolan, Garry P. [10 ]
Pevzner, Pavel A. [11 ]
Rodland, Karin D. [12 ]
Sechi, Salvatore [13 ]
Slavov, Nikolai [14 ]
Spraggins, Jeffrey M. [15 ]
Van Eyk, Jennifer E. [16 ]
Vidal, Marc [17 ]
Vogel, Christine [18 ]
Walt, David R. [19 ]
Kelleher, Neil L. [20 ]
机构
[1] Pacific Northwest Natl Lab, Environm Mol Sci Lab, Richland, WA 99354 USA
[2] Inova Hlth Syst, Inova Womens Serv Line, Falls Church, VA USA
[3] Med Univ South Carolina, Cell & Mol Pharmacol & Expt Therapeut, Charleston, SC USA
[4] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA USA
[5] Icahn Sch Med Mt Sinai, Dept Pharmacol & Syst Therapeut, New York, NY USA
[6] Brigham Young Univ, Dept Chem & Biochem, Provo, UT USA
[7] KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden
[8] Univ Washington, Dept Genome Sci, Seattle, WA USA
[9] Univ Illinois, Dept Physiol & Biophys, Chicago, IL USA
[10] Stanford Univ, Dept Pathol, Stanford, CA USA
[11] Univ Calif San Diego, Dept Comp Sci & Engn, San Diego, CA USA
[12] Pacific Northwest Natl Lab, Biol Sci Div, Richland, WA USA
[13] NIDDKD, NIH, Bethesda, MD USA
[14] Northeastern Univ, Dept Bioengn, Boston, MA USA
[15] Vanderbilt Univ, Mass Spectrometry Res Ctr, Dept Cell & Dev Biol, Nashville, TN USA
[16] Cedars Sinai Med Ctr, Adv Clin Biosyst Inst, Dept Biomed Sci, Los Angeles, CA USA
[17] Harvard Univ, Dept Genet, Cambridge, MA USA
[18] NYU, Ctr Genom & Syst Biol, New York, NY USA
[19] Harvard Univ, Brigham & Womens Hosp, Harvard Med Sch, Dept Pathol,Wyss Inst, Boston, MA USA
[20] Northwestern Univ, Dept Chem, Evanston, IL 60208 USA
基金
瑞典研究理事会; 美国国家卫生研究院;
关键词
IMAGING MASS-SPECTROMETRY; EXTRACELLULAR-MATRIX; SINGLE; QUANTIFICATION; STRATEGIES;
D O I
10.1016/j.mcpro.2022.100254
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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页数:13
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共 106 条
  • [1] A high-stringency blueprint of the human proteome
    Adhikari, Subash
    Nice, Edouard C.
    Deutsch, Eric W.
    Lane, Lydie
    Omenn, Gilbert S.
    Pennington, Stephen R.
    Paik, Young-Ki
    Overall, Christopher M.
    Corrales, Fernando J.
    Cristea, Ileana M.
    Van Eyk, Jennifer E.
    Uhlen, Mathias
    Lindskog, Cecilia
    Chan, Daniel W.
    Bairoch, Amos
    Waddington, James C.
    Justice, Joshua L.
    LaBaer, Joshua
    Rodriguez, Henry
    He, Fuchu
    Kostrzewa, Markus
    Ping, Peipei
    Gundry, Rebekah L.
    Stewart, Peter
    Srivastava, Sanjeeva
    Srivastava, Sudhir
    Nogueira, Fabio C. S.
    Domont, Gilberto B.
    Vandenbrouck, Yves
    Lam, Maggie P. Y.
    Wennersten, Sara
    Vizcaino, Juan Antonio
    Wilkins, Marc
    Schwenk, Jochen M.
    Lundberg, Emma
    Bandeira, Nuno
    Marko-Varga, Gyorgy
    Weintraub, Susan T.
    Pineau, Charles
    Kusebauch, Ulrike
    Moritz, Robert L.
    Ahn, Seong Beom
    Palmblad, Magnus
    Snyder, Michael P.
    Aebersold, Ruedi
    Baker, Mark S.
    [J]. NATURE COMMUNICATIONS, 2020, 11 (01)
  • [2] Aebersold R, 2018, NAT CHEM BIOL, V14, P206, DOI [10.1038/NCHEMBIO.2576, 10.1038/nchembio.2576]
  • [3] The emerging landscape of single-molecule protein sequencing technologies
    Alfaro, Javier Antonio
    Bohlander, Peggy
    Dai, Mingjie
    Filius, Mike
    Howard, Cecil J.
    van Kooten, Xander F.
    Ohayon, Shilo
    Pomorski, Adam
    Schmid, Sonja
    Aksimentiev, Aleksei
    Anslyn, Eric V.
    Bedran, Georges
    Cao, Chan
    Chinappi, Mauro
    Coyaud, Etienne
    Dekker, Cees
    Dittmar, Gunnar
    Drachman, Nicholas
    Eelkema, Rienk
    Goodlett, David
    Hentz, Sebastien
    Kalathiya, Umesh
    Kelleher, Neil L.
    Kelly, Ryan T.
    Kelman, Zvi
    Kim, Sung Hyun
    Kuster, Bernhard
    Rodriguez-Larrea, David
    Lindsay, Stuart
    Maglia, Giovanni
    Marcotte, Edward M.
    Marino, John P.
    Masselon, Christophe
    Mayer, Michael
    Samaras, Patroklos
    Sarthak, Kumar
    Sepiashvili, Lusia
    Stein, Derek
    Wanunu, Meni
    Wilhelm, Mathias
    Yin, Peng
    Meller, Amit
    Joo, Chirlmin
    [J]. NATURE METHODS, 2021, 18 (06) : 604 - 617
  • [4] Extracellular Matrix Imaging of Breast Tissue Pathologies by MALDI-Imaging Mass Spectrometry
    Angel, Peggi M.
    Schwamborn, Kristina
    Comte-Walters, Susana
    Clift, Cassandra L.
    Ball, Lauren E.
    Mehta, Anand S.
    Drake, Richard R.
    [J]. PROTEOMICS CLINICAL APPLICATIONS, 2019, 13 (01)
  • [5] Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry
    Angel, Peggi M.
    Comte-Walters, Susana
    Ball, Lauren E.
    Talbot, Kacey
    Mehta, Anand
    Brockbank, Kelvin G. M.
    Drakes, Richard R.
    [J]. JOURNAL OF PROTEOME RESEARCH, 2018, 17 (01) : 635 - 646
  • [6] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [7] Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability
    Assarsson, Erika
    Lundberg, Martin
    Holmquist, Goeran
    Bjoerkesten, Johan
    Thorsen, Stine Bucht
    Ekman, Daniel
    Eriksson, Anna
    Dickens, Emma Rennel
    Ohlsson, Sandra
    Edfeldt, Gabriella
    Andersson, Ann-Catrin
    Lindstedt, Patrik
    Stenvang, Jan
    Gullberg, Mats
    Fredriksson, Simon
    [J]. PLOS ONE, 2014, 9 (04):
  • [8] Mass Cytometry Imaging for the Study of Human Diseases-Applications and Data Analysis Strategies
    Baharlou, Heeva
    Canete, Nicolas P.
    Cunningham, Anthony L.
    Harman, Andrew N.
    Patrick, Ellis
    [J]. FRONTIERS IN IMMUNOLOGY, 2019, 10
  • [9] WHEN ANTIBODIES MISLEAD: THE QUEST FOR VALIDATION
    Baker, Monya
    [J]. NATURE, 2020, 585 (7824) : 313 - 314
  • [10] BLAME IT ON THE ANTIBODIES
    Baker, Monya
    [J]. NATURE, 2015, 521 (7552) : 274 - 276