PXD023738

PXD023738 is an original dataset announced via ProteomeXchange.

Title	A workflow towards the reproducible identification and quantitation of protein carbonylation sites in human plasma
Description	Protein carbonylation has been consistently used as a marker of excessive oxidative stress and studied in the context of multiple human oxidative stress related diseases. The variety of carbonyl post-translational modifications (PTMs) and their low abundance on easily accessible diagnostic tissues (e.g., plasma) challenges their reproducible identification and quantitation. However, the use of carbonyl-specific biotinylated derivatization tags (e.g., aldehyde reactive probe, ARP) allows targeting carbonyl PTMs and enriching proteins and/or peptides carrying these modifications that facilitate their characterization. In this study, an oxidized human serum albumin protein model (OxHSA) and plasma proteins from a healthy individual were derivatized with ARP, digested with trypsin, and ARP-derivatized peptides (ARP-peptides) were enriched using biotin-avidin affinity chromatography prior to RPC-TWIMS-MS/MS analysis. The present workflow highlights previously overlooked analytical challenges, shows the use of ARP specific fragment ions to improve identification reliability of ARP-peptide identifications, and displays an extensive validation of the reproducible recovery and relative quantitation of ARP-peptides. HSA was identified as the most heavily modified protein by a variety of direct amino acid oxidation products and adducts from reactive carbonyl species (RCS). Most RCS modification sites were identified in six HSA modification hotspots (Lys10, Lys190, Lys199, Lys281, Lys432, and Lys525).
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:51:57.815.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD023738
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Juan Camilo Rojas Echeverri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-21 08:39:32	ID requested
1	2021-03-01 22:24:55	announced
2	2021-03-29 01:30:17	announced	2021-03-29: Updated publication reference for DOI(s): 10.3390/antiox10030369.
⏵ 3	2023-11-14 08:51:58	announced	2023-11-14: Updated project metadata.

10.6019/PXD023738;

submitter keyword: protein carbonylation, LC-TWIMS-MS/MS, aldehyde reactive probe (ARP), human plasma, biotin-avidin affinity

Ralf Hoffmann
contact affiliation	Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, and Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig
contact email	bioanaly@rz.uni-leipzig.de
lab head
Juan Camilo Rojas Echeverri
contact affiliation	PhD Student
contact email	juan_camilo.rojas_echeverri@uni-leipzig.de
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/2021/03/PXD023738

PRIDE project URI

• PRIDE
  1. PXD023738
     1. Label: PRIDE project
     2. Name: A workflow towards the reproducible identification and quantitation of protein carbonylation sites in human plasma