PXD038283

PXD038283 is an original dataset announced via ProteomeXchange.

Title	Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry
Description	Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In archaeological or paleontological field, PMF is known as ZooMS and is widely implement-ed to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to ten-fold the required bone sample amount (down to milligram scale) and achieves robust deamidation value calculation in a high throughput manner. These improvements rely on a 96-well plates samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious posttranslational modifi-cations production and peptide mass fingerprinting at high resolution using MALDI-FTICR (Matrix Assisted Desorption Ionization Fourier Transform Ion Cyclotron Resonance) analysis. This method was applied to the identification of a hun-dred bones of herbivores from the Middle Paleolithic site of Caours (Somme, Northern France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their oste-omorphology, as well as to more challenging bone samples consisting of small or burnt bone fragments. The obtained de-amidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:59:49.302.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	BRAY FABRICE
SpeciesList	scientific name: Cervus; NCBI TaxID: 9859; scientific name: Rhinoceros; NCBI TaxID: 9808; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796; scientific name: Castor fiber (Eurasian beaver); NCBI TaxID: 10185;
ModificationList	deamidated residue
Instrument	Bruker Daltonics solarix series; Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-22 04:07:46	ID requested
1	2023-04-28 02:59:07	announced
⏵ 2	2023-11-14 08:59:49	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Species identification, Deamidation, High-throughput, Paleoproteomics,MALDI-FTICR

Bray Fabrice
contact affiliation	MSAP UAR 3290 CNRS
contact email	fabrice.bray@univ-lille.fr
lab head
BRAY FABRICE
contact affiliation	MSAP USR 3290
contact email	fabrice.bray@univ-lille.fr
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/2023/04/PXD038283

PRIDE project URI

• PRIDE
  1. PXD038283
     1. Label: PRIDE project
     2. Name: Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry