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Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

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Book cover Mass Spectrometry Data Analysis in Proteomics

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

Abstract

Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.

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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 cofunded by FEDER under the PT2020 Partnership Agreement is acknowledged. A.S.C. is supported by Fundação para a Ciência e a Tecnologia (BPD/85569/2012). 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 & Ana Sofia Carvalho

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  1. Rune Matthiesen
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  2. Ana Sofia Carvalho
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Correspondence to Ana Sofia Carvalho .

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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., Carvalho, A.S. (2020). Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. 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_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9744-2_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9743-5

  • Online ISBN: 978-1-4939-9744-2

  • eBook Packages: Springer Protocols

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