PXD058666

PXD058666 is an original dataset announced via ProteomeXchange.

Title	Screening of protein carbonylation sites in human serum by ion mobility mass spectrometry
Description	Excessive oxidative stress, which is associated with several diseases, can trigger oxidative protein modifications, including protein carbonylation, which refers to the oxidative formation of aldehyde or keto groups in proteins. The structural diversity of these non-enzymatic reactive carbonyl groups and their low abundance pose a significant challenge to their detection and quantitation. Here, we report a strategy to identify and quantify protein carbonylation in human serum samples from 39 patients diagnosed with rheumatoid arthritis and 29 healthy donors. Reactive carbonyl groups were derivatized with aldehyde reactive probe (ARP), digested with trypsin, enriched via the biotin in ARP by avidin affinity chromatography, and analyzed by RP-HPLC-ESI-IMS-MS/MS. Ion mobility spectrometry (IMS) was used in both data dependent and independent acquisition (DDA/DIA) modes. DDA was used to generate spectral libraries of ARP-derivatized carbonylated peptides (ARP-peptides), which were used for their peptide-centric detection in DIA data. This allowed the identification of 86 manually confirmed ARP-peptides that were consistently detected in the serum samples, with 93.8% of all peak areas having a signal-to-background ratio greater than 3. Of the 32 carbonylation sites identified, 28 belonged to human serum albumin, including residues Cys58, Lys214, Lys219, Lys223, Lys456, Lys543, Lys549, and Lys565, which were identified as hotspots with multiple modification types. To the best of our knowledge, six previously unreported species were identified at these hotspots based on IMS, DIA, ARP-reporter ions, and de-novo sequencing. The 86 identified carbonylated peptides were consistently quantified in serum quality controls samples with an intra-batch reproducibility of at least 75%, considering an area coefficient of variation (CV) of less than 20%. All studied modifications were present at similar levels in patient and control samples, suggesting basal disease-independent modification levels for the selected modification within the accuracy of the quantitation.
HostingRepository	PanoramaPublic
AnnounceDate	2025-06-17
AnnouncementXML	Submission_2025-06-17_08:43:29.674.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	supported by repository but incomplete data and/or metadata
PrimarySubmitter	Juan Camilo Rojas Echeverri
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	3-deoxyglucosone; Didehydro; Dehydrated; Carbamidomethyl; Oxidation; Gln->pyro-Glu; Ammonia-loss; GG; Formyl; Deamidated; Cation:Na; Dioxidation; Carbamyl; HNE; Dethiomethyl; Hex; Methyl; Biotin; Glu->pyro-Glu
Instrument	SYNAPT G2-Si

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-07 19:49:26	ID requested
⏵ 1	2025-06-17 08:43:30	announced

Rojas Echeverri JC, Milkovska-Stamenova S, Wagner U, Hoffmann R, Screening of Protein Carbonylation Sites in Human Serum by Ion Mobility Mass Spectrometry. J Proteome Res, ():(2025) [pubmed]

submitter keyword: Carbonylation, aldehyde reactive probe (ARP), ion mobility spectrometry, DDA, DIA, human serum

Ralf Hoffmann
contact affiliation	Principal Investigator
contact email	ralf.hoffmann@bbz.uni-leipzig.de
lab head
Juan Camilo Rojas Echeverri
contact affiliation	PhD Student
contact email	juan_camilo.rojas_echeverri@uni-leipzig.de
dataset submitter

Panorama Public dataset URI