PXD002896

PXD002896 is an original dataset announced via ProteomeXchange.

Title	Mouse organ specific spectral library and DIA analysis of the plasma proteome
Description	The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that contribute to the plasma proteome homeostasis we developed a mass spectrometry based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome homeostasis.
HostingRepository	PRIDE
AnnounceDate	2015-11-23
AnnouncementXML	Submission_2016-02-04_08:45:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Simon Hauri
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-11 07:16:31	ID requested
1	2015-11-23 05:59:47	announced
⏵ 2	2016-02-04 08:45:01	announced	Updated publication reference for PubMed record(s): 26732734.

Malmstr, ö, m E, Kilsg, å, rd O, Hauri S, Smeds E, Herwald H, Malmstr, ö, m L, Malmstr, ö, m J, Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nat Commun, 7():10261(2016) [pubmed]

curator keyword: Biological

submitter keyword: Mouse, organs, plasma, DIA, sepsis

Johan Malmstrom
contact affiliation	Department of Clinical Sciences, Lund Division of Infection Medicine Sweden
contact email	johan.malmstrom@med.lu.se
lab head
Simon Hauri
contact affiliation	Lund University
contact email	simon.hauri@med.lu.se
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/2015/11/PXD002896

PRIDE project URI

• PRIDE
  1. PXD002896
     1. Label: PRIDE project
     2. Name: Mouse organ specific spectral library and DIA analysis of the plasma proteome