Quantitative analysis of mass spectrometry-based proteomics data

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

Abstract

This chapter guides the user through an analysis pipeline that includes preprocessing raw mass spectrometry data into a user-friendly quantitative protein report and statistical analysis. We use a publicly available dataset as a working example that covers two prominent strategies for mass spectrometry-based proteomics, the extensively used data-dependent acquisition (DDA) and the emerging data-independent acquisition (DIA) technology. We use MaxQuant for DDA data and Spectronaut for DIA data preprocessing. Both software packages are well-established tools in the field. We perform subsequent analysis in the R software environment which offers a large repertoire of tools for data analysis and visualization. The chapter will aid lab scientists with some familiarity with R to reproducibly analyze their experiments using state-of-the-art bioinformatics methods.
Original languageEnglish
Title of host publicationNeuromethods
PublisherHumana Press Inc.
Pages129-142
Volume146
DOIs
Publication statusPublished - 1 Jan 2019

Publication series

NameNeuromethods
ISSN (Print)0893-2336
ISSN (Electronic)1940-6045

Cite this

Pham, Thang V. ; Jimenez, Connie R. / Quantitative analysis of mass spectrometry-based proteomics data. Neuromethods. Vol. 146 Humana Press Inc., 2019. pp. 129-142 (Neuromethods).
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Quantitative analysis of mass spectrometry-based proteomics data. / Pham, Thang V.; Jimenez, Connie R.

Neuromethods. Vol. 146 Humana Press Inc., 2019. p. 129-142 (Neuromethods).

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

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