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Mass Spectrometry Data Analysis in Proteomics pp 59–77Cite as

LC-MS Spectra Processing

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 2051))

Abstract

Peak extraction from raw data is the first step in LC-MS data analysis. The quality of this procedure can have dramatic effects on the quality and accuracy of all subsequent data analysis steps such as database searches and peak quantitation. The most important and most accurately measured physical entity provided by mass spectrometers is m/z. Peak processing algorithms must extract m/z values unaffected from overlapping peaks to avoid confusing downstream algorithms. The aim of this chapter is to provide a discussion of peak processing methods and furthermore discuss some of the yet unresolved or neglected issues. The chapter mainly discusses possible software developed in R for spectra processing and free software to generate Mascot generic files (mgf—see Chapter 1).

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Acknowledgments

R.M. is supported by Fundação para a Ciência e a Tecnologia (CEEC position, 2019–2025 investigator), iNOVA4Health—UID/Multi/04462/2013, a program financially supported by Fundação para a Ciência e Tecnologia/Ministério da Educação e Ciência, through national funds and is cofunded by FEDER under the PT2020 Partnership Agreement. This work is also funded by FEDER funds through the COMPETE 2020 Programme and National Funds through FCT - Portuguese Foundation for Science and Technology under the projects number PTDC/BTM-TEC/30087/2017 and PTDC/BTM-TEC/30088/2017.

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  1. Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal

    Rune Matthiesen

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  1. Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal

    Rune Matthiesen

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Matthiesen, R. (2020). LC-MS Spectra Processing. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9744-2_2

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  • DOI: https://doi.org/10.1007/978-1-4939-9744-2_2

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  • Publisher Name: Humana, New York, NY

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