PXD039875

PXD039875 is an original dataset announced via ProteomeXchange.

Title	High-throughput mass spectrometry maps the sepsis plasma proteome and differences in response
Description	THREE ARE SOME TECH PROBLEMS WHICH WILL BE SOLVED SOON! Sepsis, the dysregulated host response to infection causing life-threatening organ dysfunction, is an unmet global health challenge. Here we apply high-throughput tandem mass spectrometry to delineate the plasma proteome for 2622 sepsis and comparator samples (non-infected critical illness, postoperative inflammation and healthy volunteers) involving 4553 liquid chromatography-mass spectrometry analyses in a single batch, at 100 samples/day. We show how this scale of data can establish shared and specific proteins, pathways and co-expression modules in sepsis, and be integrated with paired leukocyte transcriptomic data (n=837 samples) using matrix decomposition. We map the landscape of the host response in sepsis including changes over time, and identify features relating to etiology, clinical phenotypes and severity. This work reveals novel subphenotypes informative for sepsis response state, disease processes and outcome, highlights potential biomarkers, pathways and processes for drug targets, and advances a systems-based precision medicine approach to sepsis.
HostingRepository	PRIDE
AnnounceDate	2024-06-11
AnnouncementXML	Submission_2024-06-11_08:21:46.231.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roman Fischer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-06 02:52:45	ID requested
1	2024-06-06 14:14:56	announced
⏵ 2	2024-06-11 08:21:47	announced	2024-06-11: Updated project metadata.

10.1126/scitranslmed.adh0185;

Mi Y, Burnham KL, Charles PD, Heilig R, Vendrell I, Whalley J, Torrance HD, Antcliffe DB, May SM, Neville MJ, Berridge G, Hutton P, Geoghegan CG, Radhakrishnan J, Nesvizhskii AI, Yu F, Davenport EE, McKechnie S, Davies R, O'Callaghan DJP, Patel P, Del Arroyo AG, Karpe F, Gordon AC, Ackland GL, Hinds CJ, Fischer R, Knight JC, Webster N, Galley H, Taylor J, Hall S, Addison J, Roughton S, Tennant H, Guleri A, Waddington N, Arawwawala D, Durcan J, Short A, Swan K, Williams S, Smolen S, Mitchell-Inwang C, Errington E, Templeton M, Venatesh P, Ward G, McCauley M, Baudouin S, Higham C, Soar J, Grier S, Hall E, Brett S, Kitson D, Wilson R, Mountford L, Moreno J, Hall P, Hewlett J, Garrard C, Millo J, Young D, Parsons P, Smiths A, Faras-Arraya R, Soar J, Raymode P, Thompson J, Bowrey S, Kazembe S, Rich N, Andreou P, Hales D, Roberts E, Fletcher S, Rosbergen M, Glister G, Cuesta JM, Bion J, Millar J, Perry EJ, Willis H, Mitchell N, Ruel S, Carrera R, Wilde J, Nilson A, Lees S, Kapila A, Jacques N, Atkinson J, Brown A, Prowse H, Krige A, Bland M, Bullock L, Harrison D, Mills G, Humphreys J, Armitage K, Laha S, Baldwin J, Walsh A, Doherty N, Drage S, de Gordoa LO, Lowes S, Higham C, Walsh H, Calder V, Swan C, Payne H, Higgins D, Andrews S, Mappleback S, Garrard C, Watson D, McLees E, Purdy A, Stotz M, Ochelli-Okpue A, Bonner S, Whitehead I, Hugil K, Goodridge V, Cawthor L, Kuper M, Pahary S, Bellingan G, Marshall R, Montgomery H, Ryu JH, Bercades G, Boluda S, Bentley A, Mccalman K, Jefferies F, Kwok A, Maugeri N, Radhakrishnan J, Allcock A, High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response. Sci Transl Med, 16(750):eadh0185(2024) [pubmed]

submitter keyword: proteomics, mass spectrometry, plasma,Sepsis, transcriptomics, sub-phenotyping, precision medicine

Roman Fischer
contact affiliation	Target Discovery Institute University of Oxford
contact email	roman.fischer@ndm.ox.ac.uk
lab head
Roman Fischer
contact affiliation	University of Oxford
contact email	roman.fischer@ndm.ox.ac.uk
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/2024/06/PXD039875

PRIDE project URI

• PRIDE
  1. PXD039875
     1. Label: PRIDE project
     2. Name: High-throughput mass spectrometry maps the sepsis plasma proteome and differences in response