Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations.
Characterization of Proteoform Post-Translational Modifications by Top-Down and Bottom-Up Mass Spectrometry in Conjunction with Annotations.
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DOI：
10.1021/acs.jproteome.3c00207
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发表时间：
2023-10-06
影响因子：
4.4
通讯作者：
Liu, Xiaowen
中科院分区：
文献类型：
--
作者：
Chen, Wenrong;Ding, Zhengming;Zang, Yong;Liu, Xiaowen
由于基因突变、选择性剪接、翻译后修饰（PTMs）和其他变异，一个基因可以产生许多蛋白质形式。蛋白质形态中的PTMs在细胞信号传导、蛋白质降解和其他生物过程中发挥关键作用。质谱（MS）是研究蛋白质形态中PTMs的主要技术，而两种可选的质谱方法，自上而下和自下而上，具有互补的优势。两种方法的结合有可能提高PTM鉴定和表征的灵敏度和准确性。此外，蛋白质和PTM知识库，如UniProt，为PTM的表征和验证提供了有价值的信息。在这里，我们提出了一个软件管道PTM- tba （PTM表征由自上而下和自下而上的MS和注释），通过集成自上而下和自下而上的MS以及PTM注释来识别和定位proteoforms中的PTM。我们使用SW480细胞自下而上和自上而下的质谱数据的技术三副本来评估PTM-TBA。自上而下MS数据的数据库检索平均发现2000个质量偏移，其中814.5个（40.7%）与11个常见PTMs相匹配，423个定位。在自上而下MS识别的质量位移中，PTM-TBA使用自下而上MS数据和UniProt注释验证了435个质量位移。
Many proteoforms can be produced from a gene due to genetic mutations, alternative splicing, post-translational modifications (PTMs), and other variations. PTMs in proteoforms play critical roles in cell signaling, protein degradation, and other biological processes. Mass spectrometry (MS) is the primary technique for investigating PTMs in proteoforms, and two alternative MS approaches, top-down and bottom-up, have complementary strengths. The combination of the two approaches has the potential to increase the sensitivity and accuracy in PTM identification and characterization. In addition, protein and PTM knowledge bases, such as UniProt, provide valuable information for PTM characterization and verification. Here, we present a software pipeline PTM-TBA (PTM characterization by Top-down and Bottom-up MS and Annotations) for identifying and localizing PTMs in proteoforms by integrating top-down and bottom-up MS as well as PTM annotations. We assessed PTM-TBA using a technical triplicate of bottom-up and top-down MS data of SW480 cells. On average, database search of the top-down MS data identified 2000 mass shifts, 814.5 (40.7%) of which were matched to 11 common PTMs and 423 of which were localized. Of the mass shifts identified by top-down MS, PTM-TBA verified 435 mass shifts using the bottom-up MS data and UniProt annotations.
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影响因子：
7.4
作者：
Chen B;Brown KA;Lin Z;Ge Y
通讯作者：
Ge Y
DOI：
10.1016/j.bbrc.2014.02.041
发表时间：
2014-03-21
影响因子：
3.1
作者：
Catherman, Adam D.;Skinner, Owen S.;Kelleher, Neil L.
通讯作者：
Kelleher, Neil L.
影响因子：
4.4
作者：
LeDuc, Richard D.;Fellers, Ryan T.;Early, Bryan P.;Greer, Joseph B.;Thomas, Paul M.;Kelleher, Neil L.
通讯作者：
Kelleher, Neil L.
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
5.8
作者：
Kou, Qiang;Xun, Likun;Liu, Xiaowen
通讯作者：
Liu, Xiaowen