PXD006802

PXD006802 is an original dataset announced via ProteomeXchange.

Title	OxSWATH applied to the redox characterization of secretomes under oxidative stress conditions
Description	Most of the redox proteomics strategies are focused on the identification and relative quantification of cysteine oxidation changes without considering the variation in the total levels of the proteins. However, the regulation of protein synthesis and protein degradation are also associated with many of the regulatory mechanisms of the cells, being therefore important to consider the changes in total protein levels in the Post Translational Modifications (PTMs) focused analyses, such as cysteine redox characterization. This aspect was only address in the cysTMTRAQ method, which combines two types of isobaric tags in the same experiment leading to a considerable increase in the costs of the analysis. Therefore, a novel integrative approach combining the SWATH-MS method with differential alkylation using non-isotopically labeled alkylating reagents (oxSWATH) is presented, thus integrating the information regarding relative cysteine oxidation with the comparative analysis of the total protein levels in a cost effective highthrouput approach. The proposed method was tested using a redox regulated protein, and further applied to a comparative analysis of secretomes obtained under control or oxidative stress conditions to strengthen the importance of considering the changes in protein total levels. OxSWATH allowed to determine the relative proportion of reduced and reversible oxidized oxoforms of the proteins, and by considering total protein levels, to determine the total levels of each fraction, which are then used for comparative analysis. This approach can be an important tool in redox centered approaches, being able to not only analyze the overall reduce/reversible oxidized state of proteins but able to be further applied in the characterization of the different oxoforms of the individual cysteines. Moreover, since samples are acquired in SWATH-MS mode, besides the redox centered analysis, a generic differential protein expression analysis can be also performed, allowing a truly comprehensive evaluation of proteomics changes upon oxidative stimulus.
HostingRepository	PRIDE
AnnounceDate	2019-02-15
AnnouncementXML	Submission_2019-02-15_07:31:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Anjo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-26 03:36:44	ID requested
⏵ 1	2019-02-15 07:31:36	announced

Anjo SI, Melo MN, Loureiro LR, Sabala L, Castanheira P, Gr, ã, os M, Manadas B, oxSWATH: An integrative method for a comprehensive redox-centered analysis combined with a generic differential proteomics screening. Redox Biol, 22():101130(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Redoxomics

Cysteine oxidation

SWATH-MS

Differential Alkylation

Secretome

DJ-1

Bruno Manadas
contact affiliation	Center for Neuroscience and Cell Biology – University of Coimbra
contact email	bmanadas@gmail.com
lab head
Sandra Anjo
contact affiliation	​Center for Neuroscience and Cell Biology – University of Coimbra
contact email	sandra.isabel.anjo@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/02/PXD006802

PRIDE project URI

• PRIDE
  1. PXD006802
     1. Label: PRIDE project
     2. Name: OxSWATH applied to the redox characterization of secretomes under oxidative stress conditions