@inbook{af509ee9330e47d8b989af7f811b95ad,
title = "Quantitative analysis of mass spectrometry-based proteomics data",
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.",
author = "Pham, {Thang V.} and Jimenez, {Connie R.}",
year = "2019",
month = jan,
day = "1",
doi = "https://doi.org/10.1007/978-1-4939-9662-9_12",
language = "English",
volume = "146",
series = "Neuromethods",
publisher = "Humana Press Inc.",
pages = "129--142",
booktitle = "Neuromethods",
}