Comparison of spectrum similarity measures for discovery of structurally related molecules

Wout Bittremieux; Robin Schmid; Florian Huber; Justin J.J. van der Hooft; Mingxun Wang; Pieter C. Dorrestein

doi:10.5281/zenodo.6609001

Comparison of spectrum similarity measures for discovery of structurally related molecules

Wout Bittremieux, Robin Schmid, Florian Huber, Justin J.J. van der Hooft, Mingxun Wang, Pieter C. Dorrestein

Research output: Contribution to conference › Poster › Academic

Abstract

The cosine similarity is the most widely used approach to match near-identical tandem mass (MS/MS) spectra with each other. An adaptation thereof, the modified cosine similarity, can be used to discover non-identical but related spectra using analog searching and molecular networking. Recently, neutral loss-based spectrum alignment was introduced as a strategy to match MS/MS spectra of analog molecules.

We have systematically evaluated the performance of neutral loss matching, cosine similarity, and modified cosine similarity on a large collection of spectrum pairs of modified peptides and small molecules to assess how spectral alignment can be used for the discovery of structurally related molecules.

Original language	English
DOIs	https://doi.org/10.5281/zenodo.6609001
Publication status	Published - 8 Jun 2022
Event	70th ASMS Conference on Mass Spectrometry and Allied Topics (2022) - Minneapolis, United States Duration: 5 Jun 2022 → 9 Jun 2022

Conference

Conference	70th ASMS Conference on Mass Spectrometry and Allied Topics (2022)
Country/Territory	United States
City	Minneapolis
Period	5/06/22 → 9/06/22

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10.5281/zenodo.6609001Licence: CC BY

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title = "Comparison of spectrum similarity measures for discovery of structurally related molecules",

abstract = "The cosine similarity is the most widely used approach to match near-identical tandem mass (MS/MS) spectra with each other. An adaptation thereof, the modified cosine similarity, can be used to discover non-identical but related spectra using analog searching and molecular networking. Recently, neutral loss-based spectrum alignment was introduced as a strategy to match MS/MS spectra of analog molecules.We have systematically evaluated the performance of neutral loss matching, cosine similarity, and modified cosine similarity on a large collection of spectrum pairs of modified peptides and small molecules to assess how spectral alignment can be used for the discovery of structurally related molecules.",

author = "Wout Bittremieux and Robin Schmid and Florian Huber and {van der Hooft}, {Justin J.J.} and Mingxun Wang and Dorrestein, {Pieter C.}",

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T1 - Comparison of spectrum similarity measures for discovery of structurally related molecules

AU - Bittremieux, Wout

AU - Schmid, Robin

AU - Huber, Florian

AU - van der Hooft, Justin J.J.

AU - Wang, Mingxun

AU - Dorrestein, Pieter C.

PY - 2022/6/8

Y1 - 2022/6/8

N2 - The cosine similarity is the most widely used approach to match near-identical tandem mass (MS/MS) spectra with each other. An adaptation thereof, the modified cosine similarity, can be used to discover non-identical but related spectra using analog searching and molecular networking. Recently, neutral loss-based spectrum alignment was introduced as a strategy to match MS/MS spectra of analog molecules.We have systematically evaluated the performance of neutral loss matching, cosine similarity, and modified cosine similarity on a large collection of spectrum pairs of modified peptides and small molecules to assess how spectral alignment can be used for the discovery of structurally related molecules.

AB - The cosine similarity is the most widely used approach to match near-identical tandem mass (MS/MS) spectra with each other. An adaptation thereof, the modified cosine similarity, can be used to discover non-identical but related spectra using analog searching and molecular networking. Recently, neutral loss-based spectrum alignment was introduced as a strategy to match MS/MS spectra of analog molecules.We have systematically evaluated the performance of neutral loss matching, cosine similarity, and modified cosine similarity on a large collection of spectrum pairs of modified peptides and small molecules to assess how spectral alignment can be used for the discovery of structurally related molecules.

U2 - 10.5281/zenodo.6609001

DO - 10.5281/zenodo.6609001

M3 - Poster

T2 - 70th ASMS Conference on Mass Spectrometry and Allied Topics (2022)

Y2 - 5 June 2022 through 9 June 2022

ER -

Comparison of spectrum similarity measures for discovery of structurally related molecules

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