Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics?
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DOI：
10.1021/acs.jproteome.1c00894
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发表时间：
2022-04-01
影响因子：
4.4
通讯作者：
MacCoss MJ
中科院分区：
文献类型：
--
作者：
Plubell DL;Käll L;Webb-Robertson BJ;Bramer LM;Ives A;Kelleher NL;Smith LM;Montine TJ;Wu CC;MacCoss MJ
自下而上的蛋白质组学提供了肽测量，并且对于将蛋白质组学转移到大规模分析中非常宝贵。通常，通过在蛋白质推断和/或简约性之后将肽量聚集到蛋白质组中来报告每个蛋白质编码基因的单个定量值。然而，考虑到RNA剪接和翻译后蛋白质修饰的复杂性，假设映射到单个蛋白质编码基因的所有肽将表现出相同的定量反应是过于简单化的。如果假设来自蛋白质编码序列的所有肽都代表相同的蛋白质，我们可能会错过重要的生物学差异的发现。为了捕捉现有的蛋白质型的贡献，我们需要重新考虑将蛋白质值聚合为每个蛋白质编码基因的单个量的做法。
Bottom-up proteomics provides peptide measurements and has been invaluable for moving proteomics into large-scale analyses. Commonly, a single quantitative value is reported for each protein coding gene by aggregating peptide quantities into protein groups following protein inference and/or parsimony. However, given the complexity of both RNA splicing and post-translational protein modification, it is overly simplistic to assume that all peptides that map to a singular protein coding gene will demonstrate the same quantitative response. By assuming all peptides from a protein coding sequence are representative of the same protein we may miss the discovery of important biological differences. To capture the contributions of existing proteoforms, we need to reconsider the practice of aggregating protein values to a single quantity per protein coding gene.
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影响因子：
3.7
作者：
Gold L;Ayers D;Bertino J;Bock C;Bock A;Brody EN;Carter J;Dalby AB;Eaton BE;Fitzwater T;Flather D;Forbes A;Foreman T;Fowler C;Gawande B;Goss M;Gunn M;Gupta S;Halladay D;Heil J;Heilig J;Hicke B;Husar G;Janjic N;Jarvis T;Jennings S;Katilius E;Keeney TR;Kim N;Koch TH;Kraemer S;Kroiss L;Le N;Levine D;Lindsey W;Lollo B;Mayfield W;Mehan M;Mehler R;Nelson SK;Nelson M;Nieuwlandt D;Nikrad M;Ochsner U;Ostroff RM;Otis M;Parker T;Pietrasiewicz S;Resnicow DI;Rohloff J;Sanders G;Sattin S;Schneider D;Singer B;Stanton M;Sterkel A;Stewart A;Stratford S;Vaught JD;Vrkljan M;Walker JJ;Watrobka M;Waugh S;Weiss A;Wilcox SK;Wolfson A;Wolk SK;Zhang C;Zichi D
通讯作者：
Zichi D
影响因子：
4.4
作者：
Dermit M;Peters-Clarke TM;Shishkova E;Meyer JG
通讯作者：
Meyer JG
影响因子：
7
作者：
Arshad, Osama A.;Danna, Vincent;McDermott, Jason E.
通讯作者：
McDermott, Jason E.
影响因子：
3.4
作者：
Matzke, Melissa M.;Brown, Joseph N.;Gritsenko, Marina A.;Metz, Thomas O.;Pounds, Joel G.;Rodland, Karin D.;Shukla, Anil K.;Smith, Richard D.;Waters, Katrina M.;McDermott, Jason E.;Webb-Robertson, Bobbie-Jo
通讯作者：
Webb-Robertson, Bobbie-Jo
DOI：
10.1073/pnas.1217238110
发表时间：
2013-03-19
影响因子：
11.1
作者：
Johansson, Asa;Enroth, Stefan;Gyllensten, Ulf
通讯作者：
Gyllensten, Ulf