Abstract
Phosphoproteomics has drawn great attention of biologist since phosphorylation is proven to play an important role in regulation of proteins. Mass spectrometry technology has helped with the development of phosphoproteomics due to its ability in generating large amount of detailed information after analyzing the phosphoproteome samples. However, interpreting the phosphoproteome data deprived from mass spectrometry can be time-consuming. Here, we introduced a free R language-based platform which can be used in accelerating phosphoproteome data analysis. This platform has integrated different functions and methods which are popularly used in phosphoproteome data analysis, so users can customize their analysis according to their demands.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Lee SC, Lan W-Z, Kim B-G et al (2007) A protein phosphorylation/dephosphorylation network regulates a plant potassium channel. Proc Natl Acad Sci U S A 104(40):15959–15964
Moorhead G, Douglas P, Cotelle V et al (1999) Phosphorylation-dependent interactions between enzymes of plant metabolism and 14-3-3 proteins. Plant J 18(1):1–12
Schwessinger B, Roux M, Kadota Y et al (2011) Phosphorylation-dependent differential regulation of plant growth, cell death, and innate immunity by the regulatory receptor-like kinase BAK1. PLoS Genet 7(4):e1002046
Bodenmiller B, Mueller LN, Mueller M et al (2007) Reproducible isolation of distinct, overlap** segments of the phosphoproteome. Nat Methods 4(3):231–237
Ficarro SB, McCleland ML, Stukenberg PT et al (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20(3):301–305
Mann M, Ong S-E, Grønborg M et al (2002) Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol 20(6):261–268
Zhai B, Villén J, Beausoleil SA et al (2008) Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res 7(4):1675–1682
Griffin NM, Yu J, Long F et al (2010) Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat Biotechnol 28(1):83–89
Journet E-P, Bligny R, Douce R (1986) Biochemical changes during sucrose deprivation in higher plant cells. J Biol Chem 261(7):3193–3199
Zauber H, Schulze WX (2012) Proteomics wants cRacker: automated standardized data analysis of LC–MS derived proteomic data. J Proteome Res 11(11):5548–5555
Mortensen P, Gouw JW, Olsen JV et al (2010) MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res 9(1):393–403
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
He, M., Li, Z. (2021). The Application of an R Language-Based Platform cRacker for Phosphoproteomics Data Analysis. In: Wu, X.N. (eds) Plant Phosphoproteomics. Methods in Molecular Biology, vol 2358. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1625-3_16
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1625-3_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1624-6
Online ISBN: 978-1-0716-1625-3
eBook Packages: Springer Protocols