PXD045027

PXD045027 is an original dataset announced via ProteomeXchange.

Title	Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses
Description	# Description of data generation and experimental procedure Six bones from La Draga (Spain, Holocene, samples LD_01 to LD_06) and Baiyisha Karst Cave (China, Pleistocene, samples BKC_07 to BKC_12) were sampled for the purpose of this study. Initial sampling was divided into three sub-samples for the three digestion duration tested here (site code_sample number_3h, site code_sample number_6h and site code_sample number_18h). Samples were then processed according to the ZooMS protocol: they were demineralised in 0.6 M hydrochloric acid (HCl) for 24 hours. The HCl supernatant was then removed and samples were rinsed thrice in 100 μL ammonium bicarbonate (50 mM, NH4HCO3, hereafter AmBic) for subsequent gelatinisation in a final volume of 100 μL AmBic for one hour at 65C. Following gelatinisation, the 100 μL AmBic solution was transferred to a new microtube, to which 0.8 μg trypsin (Promega) was added for incubation at 37 °C, with mild agitation at 300 rpm (VWR, Thermal Shake lite). Digestion occurred for either 3, 6, or 18 hours. To stop trypsin digestion, 2 μL of 5% trifluoroacetic acid (TFA) was added to each sample. The digested extracts were then split in two parts for separate analyses via matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-ToF MS) and liquid-chromatography tandem mass spectrometry (LC-MS/MS). To assess any potential contamination by non-endogenous peptides, we performed extraction of laboratory blanks alongside the samples for each enzymatic digestion condition.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:33:26.022.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frido Welker
SpeciesList	scientific name: Bovinae; NCBI TaxID: 27592;
ModificationList	hydroxylated proline; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-01 06:04:11	ID requested
1	2024-03-14 07:40:42	announced
⏵ 2	2024-10-22 06:33:26	announced	2024-10-22: Updated project metadata.

10.1016/J.ISCI.2024.109432;

submitter keyword: Digestion duration, ZooMS, Skeletal proteomics, Sustainability,Palaeoproteomics, SPIN

Frido Welker
contact affiliation	Globe Institute, University of Copenhagen
contact email	frido.welker@sund.ku.dk
lab head
Frido Welker
contact affiliation	Globe Institute, University of Copenhagen
contact email	frido.welker@sund.ku.dk
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/2024/03/PXD045027

PRIDE project URI

• PRIDE
  1. PXD045027
     1. Label: PRIDE project
     2. Name: Increasing sustainability in palaeoproteomics by optimizing digestion times for large-scale archaeological bone analyses