BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring

Thomas V Harwood; Daniel G C Treen; Mingxun Wang; Wibe de Jong; Trent R Northen; Benjamin P Bowen

doi:10.1038/s41598-023-40496-9

BLINK enables ultrafast tandem mass spectrometry cosine similarity scoring

Sci Rep. 2023 Aug 18;13(1):13462. doi: 10.1038/s41598-023-40496-9.

Authors

Thomas V Harwood¹, Daniel G C Treen¹, Mingxun Wang², Wibe de Jong³, Trent R Northen¹, Benjamin P Bowen⁴

Affiliations

¹ Environmental Genomics and Systems Biology Division, The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA.
² Department of Computer Science and Engineering, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
³ Computational Chemistry, Materials and Climate Group, Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA.
⁴ Environmental Genomics and Systems Biology Division, The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA. bpbowen@lbl.gov.

Abstract

Metabolomics has a long history of using cosine similarity to match experimental tandem mass spectra to databases for compound identification. Here we introduce the Blur-and-Link (BLINK) approach for scoring cosine similarity. By bypassing fragment alignment and simultaneously scoring all pairs of spectra using sparse matrix operations, BLINK is over 3000 times faster than MatchMS, a widely used loop-based alignment and scoring implementation. Using a similarity cutoff of 0.7, BLINK and MatchMS had practically equivalent identification agreement, and greater than 99% of their scores and matching ion counts were identical. This performance improvement can enable calculations to be performed that would typically be limited by time and available computational resources.