Mass spectra alignment using virtual lock-masses

Francis Brochu,Alexandre Drouin,Francine Durocher,Dave Richard,François Laviolette,Caroline Diorio,Dominic Gagnon,Jacques Corbeil,Pier-Luc Plante,Mario Marchand

doi:10.1038/s41598-019-44923-8

Francis Brochu, Alexandre Drouin + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-44923-8

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Abstract

Mass spectrometry is a valued method to evaluate the metabolomics content of a biological sample. The recent advent of rapid ionization technologies such as Laser Diode Thermal Desorption (LDTD) and Direct Analysis in Real Time (DART) has rendered high-throughput mass spectrometry possible. It is used for large-scale comparative analysis of populations of samples. In practice, many factors resulting from the environment, the protocol, and even the instrument itself, can lead to minor discrepancies between spectra, rendering automated comparative analysis difficult. In this work, a sequence/pipeline of algorithms to correct variations between spectra is proposed. The algorithms correct multiple spectra by identifying peaks that are common to all and, from those, computes a spectrum-specific correction. We show that these algorithms increase comparability within large datasets of spectra, facilitating comparative analysis, such as machine learning.

Highlights

Mass spectrometry (MS) is a widely used technique for acquiring data on the metabolome or the proteome of individuals[1,2]
The virtual lock mass (VLM) detection algorithm was independently applied to (1) every spectrum in the dataset, (2) only the spectra acquired on the first day, and (3) only the spectra acquired on the second day
This window size was determined by the procedure described in the Methods section, being the w that yielded the largest number of isolated VLMs on the entire dataset

Summary

Introduction

Mass spectrometry (MS) is a widely used technique for acquiring data on the metabolome or the proteome of individuals[1,2]. Novel ionization technologies have emerged, facilitating the high-throughput acquisition of mass spectra[10] Technologies such as Laser Diode Thermal Desorption (LDTD) or Direct Analysis in Real Time (DART), allow for the rapid acquisition of large datasets. Three algorithms have been proposed to address this problem, mainly affecting Time-of-Flight mass spectrometers These include the work of Tibshirani et al.[13], Jeffries[14], and Tracy et al.[15]. Jeffries’ algorithm is more appropriate for this problem This method uses cubic splines to recalibrate spectra, based on the shifts between observed peaks and known reference masses. A similar algorithm has been proposed by Barry et al (2013) for Fourier-Transform Mass Spectrometry[16] This approach uses ambient ions in order to correct the spectra using known reference masses. Correspondence and requests for materials should be addressed to F.B.

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Conclusion