PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches.
PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches.
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PTMSearchPlus：通过集成准确的完整蛋白质质量和自下而上的质谱数据搜索来自动蛋白质识别和翻译后修饰表征的软件工具。
DOI：
10.1021/ac901163c
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发表时间：
2009
影响因子：
7.4
通讯作者：
Hettich,RobertL
中科院分区：
文献类型：
--
作者：
Kertesz,Vilmos;Connelly,HeatherM;Erickson,BrianK;Hettich,RobertL
PTMSearchPlus是一个软件工具，用于自动整合准确的完整蛋白质质量(AIPM)和自下而上(BU)的质谱搜索/数据，以便既可以自信地识别完整的蛋白质，又可以表征它们的翻译后修饰(PTM)。PTMSearchPlus的开发是为了有效地将高分辨率完整蛋白质分子质量与自下而上的多肽MS/MS数据相结合。PTMSearchPlus需要从同一蛋白质混合物中收集的完整蛋白质和蛋白水解肽的质谱图、FASTA蛋白质数据库以及可指定其类型和范围的可能的蛋白质组分的选择作为输入。PTMSearchPlus的输出是与AIPM数据匹配的完整和修饰蛋白质的列表，这些蛋白质与BU搜索发现的各自的多肽相匹配。该列表还包含可用于进一步评估或重新过滤结果的蛋白质和肽序列覆盖信息、分数等。当所列出的蛋白质或多肽被选择时，相应的和注释的AIPM和BU质谱图也被显示用于目视检查。这些和其他控制确保用户可以手动评估、修改(例如，移除明显的假阳性、低质量光谱等)，并在必要时保存自动搜索的结果。当探测多个PTM时，由于BU搜索中可能的多肽候选数量的指数增长，除了集成方法之外，还讨论了通过限制BU搜索中肽上可能的PTM的总数或通过执行AIPM预测BU搜索在搜索速度上的优势。PTMSearchPlus的特征是用来自大肠杆菌的蛋白质标准混合物和复杂蛋白质混合物来演示的。实验数据显示了耦合AIPM和BU数据集的独特优势，这对两种方法都是互惠互利的。即，AIPM数据可以确认在BU搜索中没有遗漏PTM多肽，而BU搜索确定了PTM的位置。仅使用AIPM搜索无法获得此信息。
PTMSearchPlus is a software tool for the automated integration of accurate intact protein mass (AIPM) and bottom-up (BU) mass spectra searches/data in order to both confidently identify the intact proteins and to characterize their post-translational modifications (PTMs). The development of PTMSearchPlus was motivated by the desire to effectively integrate high-resolution intact protein molecular masses with bottom-up peptide MS/MS data. PTMSearchPlus requires as input both intact protein and proteolytic peptide mass spectra collected from the same protein mixture, a FASTA protein database, and a selection of possible PTMs, the types and ranges of which can be specified. The output of PTMSearchPlus is a list of intact and modified proteins matching the AIPM data concomitant with their respective peptides found by the BU search. This list also contains protein and peptide sequence coverage information, scores, etc. that can be used for further evaluation or refiltering of the results. Corresponding and annotated AIPM and BU mass spectra are also displayed for visual inspection when a listed protein or a peptide is selected. These and other controls ensure that the user can manually evaluate, modify (e.g., remove obvious false positives, low quality spectra etc.), and save the results of the automated search if necessary. Driven by the exponential growth in the number of possible peptide candidates in a BU search when multiple PTMs are probed, the advantages on search speed by limiting the total number of possible PTMs on a peptide in the BU search or by performing an AIPM predicted BU search are also discussed in addition to the integration approach. The features of PTMSearchPlus are demonstrated using both a protein standard mixture and a complex protein mixture from Escherichia coli. Experimental data revealed a unique advantage of coupling AIPM and the BU data sets that is mutually beneficial for both approaches. Namely, AIPM data can confirm that no PTM peptides were missed in a BU search, while the BU search determines the location of the PTM. This information is not available using an AIPM search alone.