Recent increases in mass spectrometry speed, sensitivity, and resolution now permit comprehensive proteomics coverage. However, the results are often hindered by sub-optimal data processing pipelines. In almost all MS/MS peptide search engines, users must limit their search space to a canonical database due to time constraints and q value considerations, but this typically does not reflect the individual genetic variations of the organism being studied. In addition, engines will nearly always assume the presence of only fully tryptic peptides and limit PTMs to a handful. Even on high-performance servers, these search engines are computationally expensive, and most users decide to dial back their search parameters. We present Bolt, a new cloud-based search engine that can search more than 900,000 protein sequences (canonical, isoform, mutations, and contaminants) with 41 post-translation modifications and N-terminal and C-terminal partial tryptic search in minutes on a standard configuration laptop. Along with increases in speed, Bolt provides an additional benefit of improvement in high-confidence identifications. Sixty-one percent of peptides uniquely identified by Bolt may be validated by strong fragmentation patterns, compared with 13% of peptides uniquely identified by SEQUEST and 6% of peptides uniquely identified by Mascot. Furthermore, 30% of unique Bolt identifications were verified by all three software on the longer gradient analysis, compared with only 20% and 27% for SEQUEST and Mascot identifications respectively. Bolt represents, to the best of our knowledge, the first fully scalable, cloud-based quantitative proteomic solution that can be operated within a user-friendly GUI interface. Data are available via ProteomeXchange with identifier PXD012700.

中文翻译：

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Bolt：几分钟之内即可通过大量蛋白质数据库进行全面MS / MS测序的新时代肽搜索引擎。

质谱速度，灵敏度和分离度的最新提高现在可以实现蛋白质组学的全面覆盖。但是，结果通常会受到次优数据处理管道的阻碍。在几乎所有的MS / MS肽搜索引擎中，由于时间限制和q值考虑，用户必须将其搜索空间限制在标准数据库中，但这通常不能反映所研究生物的个体遗传变异。此外，引擎几乎总是假设只有完全胰蛋白酶的肽存在，并将PTM限制为少数。即使在高性能服务器上，这些搜索引擎在计算上也很昂贵，并且大多数用户决定回拨其搜索参数。我们介绍了Bolt，这是一种新的基于云的搜索引擎，可以搜索900,000多种蛋白质序列（规范，同种型，突变，和污染物）在标准配置的笔记本电脑上只需几分钟即可完成41个翻译后修饰以及N端和C端部分胰蛋白酶的搜索。随着速度的提高，Bolt还提供了改进高可信度标识的其他好处。通过Bolt唯一识别的肽中有61％可以通过强片段化模式进行验证，相比之下，由SEQUEST唯一识别的肽中有13％和由Mascot唯一识别的肽中有6％。此外，在较长的梯度分析中，所有三个软件均对30％的独特Bolt标识进行了验证，而SEQUEST和Mascot标识分别仅为20％和27％。就我们所知，Bolt代表了第一个完全可扩展的，基于云的定量蛋白质组学解决方案，可以在用户友好的GUI界面中运行。数据可通过ProteomeXchange获得，其标识符为PXD012700。