PXD020462-2

PXD020462 is an original dataset announced via ProteomeXchange.

Title	Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum.
Description	In search of markers for protein aging, we used an extraordinary test case of human bones from the excavations sites of Pompei and Herculaneum (79 AD), analyzed by a shotgun proteomic approach using LC-MS/MS. Human bones from Scalandrone Bay (II sec AD, another volcanic area, yet not related to Vesuvius eruption were also analysed for the comparison of the PTMs provoked from a volcanic ground to an almost coeval standard burial condition. In addition, already published archaeological bones, approximately 17 centuries younger than the test case, were used as control samples. Deamidation of asparagine and glutamine was examined as a now widely considered aging molecular marker. Deamidation profile was quite robust for samples with a similar age whereas the fewer proteins were detected, the more degraded the sample were found to be. Positional investigation of deamidation in the polypeptide sequence of collagen type I revealed that some zones are more susceptible to deamidation than others. Back bone cleavage analysis confirmed that some zones apart from deamidation are more susceptible to spontaneous hydrolysis too. Analysis of post-translational modifications showed higher advanced glycation products of lysine and arginines in the samples of Pompeii and Herculaneum. Furthermore, oxidative products of methionine, histidine and the conversion of ST to glycine were also detected. Interestingly, multiple oxidation products of proline and dehydration of hydroxyproline were detected for the first time, turning the scientific interest to this amino acid (P), which is usually ignored due to its natural conversion to hydroxyproline. As a matter of fact, we can observe that collagen degradation in bones from Pompeii and Herculaneum underwent different degradation processes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:23:53.422.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Georgia Ntasi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	dihydroxylated residue; L-ornithine (Arg); N6-carboxymethyl-L-lysine; Oxohistidine (from histidine); dehydrated residue; N6-1-carboxyethyl-L-lysine; methylglyoxal arginine adduct (+54 amu); formylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-20 22:11:58	ID requested
1	2021-07-10 03:56:11	announced
⏵ 2	2024-10-22 05:23:53	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: paleoproteomics,Human bones, Pompeii, AGEs,Deamidation (NQ),Vesuvius,79 AD Herculaneum, Shotgun proteomics

Leila Birolo
contact affiliation	Department of Chemical Sciences, University of Federico II,Naples, Italy
contact email	birolo@unina.it
lab head
Georgia Ntasi
contact affiliation	University of Naples "Federico II"
contact email	georgiant91@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/2021/07/PXD020462

PRIDE project URI

• PRIDE
  1. PXD020462
     1. Label: PRIDE project
     2. Name: Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum.