The Synergies of Mass Spectrometry and Informatics and PaSER: Parallel Database Search Engine in Real-Time and beyond

This webinar took place on June 02, 2020

Webinar Overview

Duration: 37 minutes

The Synergies of Mass Spectrometry and Informatics
John R. Yates, III
The Scripps Research Institute

Mass spectrometry has always had a powerful synergy with computers. Computers have pushed mass spectrometry forward at key junctures in its history from data collection to instrument operation to data analysis. Proteomics was enabled by both tandem mass spectrometry and informatics to rapidly assign amino acid sequences to spectra. As instrumentation has become more powerful informatic capabilities have grown to keep pace with increases in data production and data types. Sophisticated workflows are used to process proteomic experiments that encompass search, quantitation, and statistical processing of data. As new features are added to mass spectrometers like ion mobility this provides additional capability for collecting data and information for interpreting peptides and peptide features. IP2 is a proteomic platform that creates a workflow combining GPU powered search, flexible quantitation, and statistical analysis of data.

Part 2:
PASER: Parallel Database Search Engine in Real-Time and beyond
Robin Park
Bioinformatics Yates Lab, Scripps Research and CEO Integrated Proteomics Applications

We developed PaSER (Parallel Database Search Engine in Real-Time), which performs database searching in parallel with data acquisition on a high-speed timsTOF Pro mass spectrometer. To perform a database search in real-time, PaSER adopts a fast IP2-GPU ProLuCID search engine. Using PaSER, we demonstrate the simultaneous completion of database searching and MS spectra acquisition. The PaSER search engine can keep up with the 120Hz MS/MS-acquisition speed of the timsTOF Pro instrument, saving significant time by elimination of separate data extraction and protein database search steps, thus enabling true high-throughput proteomics data analysis in an automated way. PaSER is scalable and can perform searches on data from multiple timsTOF instruments without compromising the search speed on any of the data analyses.

Key learning objectives:

  • Bioinformatics capabilities of the timsTOF Pro
  • A scalable, ultrafast search engine with IP2GPU
  • A complete infrastructure for proteomics data analysis
  • Real-time search possibilities

Who should attend:

  • Proteomics scientists
  • Pharma and biotech scientists
  • Scientists interested in efficient data analysis
  • Molecular and cellular biologist


Prof. John Yates, III
PhD, The Scripps Research Institute, Molecular Medicine, La Jolla, CA, USA

Robin Park
Director Bioinformatics Yates Lab, Scripps Research and CEO Integrated Proteomics Applications, La Jolla, CA, USA


For Research Use Only. Not for use in clinical diagnostic procedures.