PXD014877

PXD014877 is an original dataset announced via ProteomeXchange.

Title	The Proteome Landscape of the Kingdoms of Life
Description	Proteins preform the vast majority of functions in all biological domains but their large-scale investigation has lagged behind for technological reasons. Since the first essentially complete eukaryotic proteome was reported1, advances in mass spectrometry (MS)-based proteomics2 have enabled increasingly comprehensive identification and quantification of the human proteome3456. However, there are few comparisons across species, especially compared to genomics initiatives7. Here, we employ an advanced proteomics workflow, in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system, for the in-depth measurement of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a foundation for machine learning, as we demonstrate by experimentally confirming predicted peptide properties of bacteroides uniformis. Our results provide a comparative view into the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the challenge of maintaining protein structure across all of life. Likewise, a constantly high fraction is involved in supplying energy resources, although the pathways range from photosynthesis through iron sulphur metabolism to carbohydrate metabolism.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:50:13.242.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Vitis vinifera (Grape); NCBI TaxID: 29760; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Dictyostelium discoideum (Slime mold); NCBI TaxID: 44689; scientific name: Triticum aestivum (Wheat); NCBI TaxID: 4565; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Danio rerio (Zebrafish) (Brachydanio rerio); NCBI TaxID: 7955; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-01 05:59:35	ID requested
1	2020-06-18 05:15:32	announced
2	2020-06-19 01:15:02	announced	2020-06-19: Updated publication reference for DOI(s): 10.1038/s41586-020-2402-x.
3	2020-07-01 22:03:42	announced	2020-06-19: Updated publication reference for DOI(s): 10.1038/s41586-020-2402-x. 2020-07-02: Updated publication reference for PubMed record(s): 32555458. 2020-07-02: Updated publication reference for DOI(s): 10.1038/s41586-020-2402-x.
⏵ 4	2023-11-14 08:50:15	announced	2023-11-14: Updated project metadata.

M, ü, ller JB, Geyer PE, Cola, ç, o AR, Treit PV, Strauss MT, Oroshi M, Doll S, Virreira Winter S, Bader JM, K, ö, hler N, Theis F, Santos A, Mann M, The proteome landscape of the kingdoms of life. Nature, 582(7813):592-596(2020) [pubmed]

submitter keyword: machine learning, mass spectrometry,Proteomics, bioinformatics, systems biology, phylogeny

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany 2NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
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/2020/06/PXD014877

PRIDE project URI

• PRIDE
  1. PXD014877
     1. Label: PRIDE project
     2. Name: The Proteome Landscape of the Kingdoms of Life