Utilizing Precursor Ion Connectivity of Different Charge States to Improve Peptide and Protein Identification in MS/MS Analysis.
Utilizing Precursor Ion Connectivity of Different Charge States to Improve Peptide and Protein Identification in MS/MS Analysis.
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DOI：
10.1021/acs.analchem.3c03061
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发表时间：
2024-01-23
影响因子：
7.4
通讯作者：
Cramer, Rainer
中科院分区：
文献类型：
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作者：
Adair, Lily R.;Jones, Ian;Cramer, Rainer
串联质谱（MS/MS）已成为多肽和蛋白质等生物分子结构分析的关键方法。在MS/MS分析中，特别是对于自上而下的蛋白质组学，普遍存在的问题是当两个或更多个前体离子被共分离和碎片化时出现嵌合光谱，从而导致复杂的MS/MS光谱，其填充有源自不同前体离子的碎片离子。由于大量的混合源碎片离子，这种类型的卷积数据通常导致低序列数据库搜索分数，其中只有一部分来自特定的前体离子。在本文中，我们提出了一种新的工作流程，该工作流程对嵌合MS/MS光谱的数据进行去卷积，提高了数据库搜索中的蛋白质搜索分数和序列覆盖率，从而提供了更可靠的肽和蛋白质鉴定。先前错误识别的蛋白质或具有不显著搜索分数的蛋白质可以在所呈现的数据采集和分析工作流程之后被正确且显著地识别，其中对于较小的前体离子（肽），搜索分数增加3-4倍，对于较大的前体离子（如完整的泛素和细胞色素C），搜索分数增加>6倍。
Tandem mass spectrometry (MS/MS) has become a key method for the structural analysis of biomolecules such as peptides and proteins. A pervasive problem in MS/MS analyses, especially for top-down proteomics, is the occurrence of chimeric spectra, when two or more precursor ions are co-isolated and fragmented, thus leading to complex MS/MS spectra that are populated with fragment ions originating from different precursor ions. This type of convoluted data typically results in low sequence database search scores due to the vast number of mixed-source fragment ions, of which only a fraction originates from a specific precursor ion. Herein, we present a novel workflow that deconvolutes the data of chimeric MS/MS spectra, improving the protein search scores and sequence coverages in database searching and thus providing a more confident peptide and protein identification. Previously misidentified proteins or proteins with insignificant search scores can be correctly and significantly identified following the presented data acquisition and analysis workflow with search scores increasing by a factor of 3–4 for smaller precursor ions (peptides) and >6 for larger precursor ions such as intact ubiquitin and cytochrome C.
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影响因子：
16.6
作者：
Cramer, Rainer;Pirkl, Alexander;Hillenkamp, Franz;Dreisewerd, Klaus
通讯作者：
Dreisewerd, Klaus
影响因子：
56.9
作者：
Melani, Rafael D.;Gerbasi, Vincent R.;Anderson, Lissa C.;Sikora, Jacek W.;Toby, Timothy K.;Hutton, Josiah E.;Butcher, David S.;Negrao, Fernanda;Seckler, Henrique S.;Srzentic, Kristina;Fornelli, Luca;Camarillo, Jeannie M.;LeDuc, Richard D.;Cesnik, Anthony J.;Lundberg, Emma;Greer, Joseph B.;Fellers, Ryan T.;Robey, Matthew T.;DeHart, Caroline J.;Forte, Eleonora;Hendrickson, Christopher L.;Abbatiello, Susan E.;Thomas, Paul M.;Kokaji, Andy, I;Levitsky, Josh;Kelleher, Neil L.
通讯作者：
Kelleher, Neil L.
影响因子：
4.4
作者：
Houel, Stephane;Abernathy, Robert;Old, William M.
通讯作者：
Old, William M.
影响因子：
7.4
作者：
Charkow, Joshua;Rost, Hannes L.
通讯作者：
Rost, Hannes L.
影响因子：
16.6
作者：
通讯作者：
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