Bolt: a New Age Peptide Search Engine for Comprehensive MS/MS Sequencing Through Vast Protein Databases in Minutes

  • Amol PrakashEmail author
  • Shadab Ahmad
  • Swetaketu Majumder
  • Conor Jenkins
  • Ben Orsburn
Research Article


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.


Mass spectrometry Proteomics Peptide Mutations Search engine MS/MS Sequencing Variants Cloud Bolt 



We would like to acknowledge Simion Kreimer, Ph.D. (Johns Hopkins University) and Dragana Lagundzin, Ph.D. (University of Nebraska) for their help with the Mascot analysis.

Supplementary material

13361_2019_2306_MOESM1_ESM.xlsx (14 kb)
Supplementary Table 1 (XLSX 13 kb)
13361_2019_2306_MOESM2_ESM.xlsx (9 kb)
Supplementary Table 2 (XLSX 8 kb)


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Copyright information

© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Optys Tech CorporationShrewsburyUSA
  2. 2.Department of BiologyHood CollegeFrederickUSA
  3. 3.Proteomic und Genomic SciencesBaltimoreUSA

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