PXD021963

PXD021963 is an original dataset announced via ProteomeXchange.

Title	species identification using bone protein
Description	Proteogenomics is an increasingly common method for species identification as it allows for rapid and inexpensive interrogation of an unknown organism’s proteome – even when the proteome is partially degraded. The proteomic method typically uses tandem mass spectrometry to survey all peptides detectable in a sample that frequently contains hundreds or thousands of proteins. Species identification is based on detection of a small numbers of species-specific peptides. Genetic analysis of proteins by mass spectrometry, however, is a developing field, and the bone proteome, typically consisting of only two proteins, pushes the limits of this technology. Nearly 20% of highly confident spectra from modern human bone samples identify non-human species when searched against a vertebrate database – as would be necessary with a fragment of unknown bone. These non-human peptides are often the result of current limitations in mass spectrometry or algorithm interpretation errors. Consequently, it is difficult to know if a “species-specific” peptide used to identify a sample is actually present in that sample. Here we evaluate the causes of peptide sequence errors and propose an unbiased, probabilistic approach to determine the likelihood that a species is correctly identified from bone without relying on species-specific peptides.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_10:06:45.902.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Erin Butler
SpeciesList	scientific name: Ovis aries; NCBI TaxID: 9940; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Canis lupus; NCBI TaxID: 9612; scientific name: Odocoileus virginianus; NCBI TaxID: 9874; scientific name: Equus caballus (Horse); NCBI TaxID: 9796; scientific name: Felis catus; NCBI TaxID: 9685; scientific name: Marmota monax; NCBI TaxID: 9995; scientific name: Tursiops truncatus; NCBI TaxID: 9739; scientific name: Macaca mulatta; NCBI TaxID: 9544; scientific name: Didelphis virginiana; NCBI TaxID: 9267; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Ursus americanus; NCBI TaxID: 9643; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Lontra canadensis; NCBI TaxID: 76717; scientific name: Sciurus carolinensis; NCBI TaxID: 30640;
ModificationList	No PTMs are included in the dataset
Instrument	4800 Proteomics Analyzer

Revision	Datetime	Status	ChangeLog Entry
0	2020-10-14 01:33:48	ID requested
⏵ 1	2021-09-09 10:06:46	announced

Yang H, Butler ER, Monier SA, Teubl J, Feny, ö D, Ueberheide B, Siegel D, A predictive model for vertebrate bone identification from collagen using proteomic mass spectrometry. Sci Rep, 11(1):10900(2021) [pubmed]

submitter keyword: bone, LC-MS/MS MALDI

Donald Siegel
contact affiliation	Office of the Chief Medical Examiner New York City
contact email	dsiegel@ocme.nyc.gov
lab head
Erin Butler
contact affiliation	Office of the Chief Medical Examiner New York City
contact email	erbutler@ocme.nyc.gov
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/2021/09/PXD021963

PRIDE project URI

• PRIDE
  1. PXD021963
     1. Label: PRIDE project
     2. Name: species identification using bone protein