Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.
Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.
复制标题
比较自上而下的蛋白质相识别：反卷积，PRSM重叠和PTM检测。
DOI：
10.1021/acs.jproteome.2c00673
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发表时间：
2023-07-07
影响因子：
4.4
通讯作者：
Chamot-Rooke, Julia
中科院分区：
文献类型：
--
作者：
Tabb, David L.;Jeong, Kyowon;Druart, Karen;Gant, Megan S.;Brown, Kyle A.;Nicora, Carrie;Zhou, Mowei;Couvillion, Sneha;Nakayasu, Ernesto;Williams, Janet E.;Peterson, Haley K.;McGuire, Michelle K.;McGuire, Mark A.;Metz, Thomas O.;Chamot-Rooke, Julia
关键词：
从蛋白质型的复杂混合物产生自上而下的串联质谱（MS/MS）受益于分馏、分离、片段化和质量分析的改进。将MS/MS与序列匹配的算法已经经历了并行的演变，光谱比对和匹配计数方法都产生了高质量的蛋白质组-光谱匹配（PrSM）。本研究评估了最先进的自上而下识别算法（ProSight PD，TopPIC，MSPathFinderT和pTop）的PrSM产量，同时控制错误发现率。我们在ThermoFisher Orbitrap-class和Bruker maXis Q-TOF数据（PXD 033208）中评估了去卷积引擎（ThermoFisher Xtract、Bruker AutoMSn、Matrix Science Mascot Distiller、TopFD和FLASHDeconv），以产生一致的前体电荷和质量测定。最后，我们在牛乳（PXD 031744）和人卵巢组织的蛋白质型中寻找翻译后修饰（PTM）。当代的鉴定工作流程产生了优异的PrSM产量，尽管来自这四个管道的所有鉴定的蛋白质型中约有一半仅特定于一个工作流程。反卷积算法对前体质量和电荷不一致，导致识别可变性。PTM的检测在算法之间不一致。在牛乳中，由pTop和TopMG产生的PrSM中有18%是单磷酸化的，但对于一种算法，这一百分比下降到1%。应用多个搜索引擎可以对实验进行更全面的评估。自上而下的算法将受益于更大的互操作性。
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate. We evaluated deconvolution engines (ThermoFisher Xtract, Bruker AutoMSn, Matrix Science Mascot Distiller, TopFD, and FLASHDeconv) in both ThermoFisher Orbitrap-class and Bruker maXis Q-TOF data (PXD033208) to produce consistent precursor charges and mass determinations. Finally, we sought post-translational modifications (PTMs) in proteoforms from bovine milk (PXD031744) and human ovarian tissue. Contemporary identification workflows produce excellent PrSM yields, although approximately half of all identified proteoforms from these four pipelines were specific to only one workflow. Deconvolution algorithms disagree on precursor masses and charges, contributing to identification variability. Detection of PTMs is inconsistent among algorithms. In bovine milk, 18% of PrSMs produced by pTop and TopMG were singly phosphorylated, but this percentage fell to 1% for one algorithm. Applying multiple search engines produces more comprehensive assessments of experiments. Top-down algorithms would benefit from greater interoperability.
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影响因子：
14.9
作者：
Harshman SW;Young NL;Parthun MR;Freitas MA
通讯作者：
Freitas MA
影响因子：
--
作者：
Holman JD;Ma ZQ;Tabb DL
通讯作者：
Tabb DL
影响因子：
4.4
作者：
Peng Y;Chen X;Zhang H;Xu Q;Hacker TA;Ge Y
通讯作者：
Ge Y
DOI：
10.1016/j.jasms.2007.01.010
发表时间：
2007-05-01
影响因子：
3.2
作者：
Falkner, Jayson A.;Kachman, Maureen;Andrews, Philip C.
通讯作者：
Andrews, Philip C.
影响因子：
7
作者：
Frottin, Frederic;Martinez, Aude;Meinnel, Thierry
通讯作者：
Meinnel, Thierry