Please use this identifier to cite or link to this item: https://hdl.handle.net/10316/107322
Title: oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening
Authors: Anjo, Sandra I. 
Melo, Matilde N. 
Loureiro, Liliana R. 
Sabala, Lúcia 
Castanheira, Pedro
Grãos, Mário 
Manadas, Bruno 
Issue Date: Apr-2019
Publisher: Elsevier
Project: PTDC/NEU-NMC/0205/2012 
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID/NEU/04539/2013 
SAICTPAC/0010/2015 
PTDC/NEU-SCC/7051/2014 
PTDC/MED-NEU/27946/2017 
Serial title, monograph or event: Redox Biology
Volume: 22
Abstract: Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation without considering the variation in the total levels of the proteins. However, protein synthesis and protein degradation also belong to the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in PTMs-focused analyses, such as cysteine redox characterization. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using a combination of commonly available alkylating reagents (oxSWATH) is presented, by which it is possible to integrate the information regarding relative cysteine oxidation with the analysis of the total protein levels in a cost-effective high-throughput approach. The proposed method was tested using a redox-regulated protein and further applied to a comparative analysis of secretomes obtained from cells cultured under control or oxidative stress conditions to strengthen the importance of considering the overall proteome changes. Using the OxSWATH method it was possible to determine both the relative proportion of reduced and reversible oxidized oxoforms, as well as the total levels of each oxoform by taking into consideration the total levels of the protein. Therefore, using OxSWATH the comparative analyses can be performed at two different levels by considering the relative proportion or the total levels at both peptide and protein level. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can also be performed, allowing a truly comprehensive evaluation of proteomics changes upon the oxidative stimulus. Data are available via ProteomeXchange and SWATHAtlas with the identifiers PXD006802, PXD006802, and PASS01210.
URI: https://hdl.handle.net/10316/107322
ISSN: 22132317
DOI: 10.1016/j.redox.2019.101130
Rights: openAccess
Appears in Collections:FMUC Medicina - Artigos em Revistas Internacionais
I&D CNC - Artigos em Revistas Internacionais

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