Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States.
Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, United States.
J Proteome Res. 2021 Apr 2;20(4):1928-1935. doi: 10.1021/acs.jproteome.0c00952. Epub 2021 Mar 2.
Top-down mass spectrometry (TD-MS) of peptides and proteins results in product ions that can be correlated to polypeptide sequence. Fragments can either be terminal fragments, which contain either the N- or the C-terminus, or internal fragments that contain neither termini. Normally, only terminal fragments are assigned due to the computational difficulties of assigning internal fragments. Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complementary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum. Data are available via the MassIVE community resource with the identifiers MSV000086788 and MSV000086789.
自上而下的肽和蛋白质的质谱分析（TD-MS）产生的产物离子可以与多肽序列相关联。片段可以是末端片段，包含 N 端或 C 端，也可以是不包含两端的内部片段。通常，由于分配内部片段的计算困难，只能分配末端片段。在这里，我们描述了 ClipsMS，这是一种可以分配由自上而下的 MS 碎片化产生的末端和内部片段的算法。此外，ClipsMS 可用于定位蛋白质序列上的各种修饰。使用 ClipsMS 分配 TD-MS 生成的产物离子，我们证明对于脱辅基肌红蛋白，包含内部片段可将序列覆盖率提高到 78%。有趣的是，许多内部片段覆盖与末端片段互补的区域，从而增强了从单个自上而下的质谱中提取的信息。使用 ClipsMS 通过末端和内部片段匹配对氧化脱辅基肌红蛋白进行分析，证实了两个蛋氨酸残基上氧化位点的位置。内部片段对于自上而下的蛋白质片段分析是有益的，并且 ClipsMS 可以成为分配自上而下的质谱中存在的末端和内部片段的有价值的工具。数据可通过 MassIVE 社区资源获得，标识符为 MSV000086788 和 MSV000086789。
