PXD017385

PXD017385 is an original dataset announced via ProteomeXchange.

Title	Sample multiplexing for targeted pathway proteomics: application to aging mice
Description	Pathway proteomics strategies measure protein expression changes in specific cellular processes that carry out related functions. Using targeted TMT-based sample multiplexing, hundreds of proteins can be quantified across 10 or more samples simultaneously. To facilitate these highly complex experiments, we introduce a strategy that provides complete control over targeted sample multiplexing experiments, termed Tomahto, and present its first implementation on the Orbitrap Tribrid mass spectrometer platform. Importantly, this software monitors via the external desktop computer to the data stream and inserts optimized MS2 and MS3 scans in real time based on an application programming interface (API) with the mass spectrometer. Hundreds of proteins of interest from diverse biological samples can be targeted and accurately quantified in a sensitive and high throughput fashion. It achieves comparable, if not better, sensitivity as deep fractionation and requires minimal total sample input (~10 µg). As a proof-of-principle experiment, we selected 4 pathways important in metabolism- and inflammation-related processes (260 proteins/520 peptides) and measured their abundance across 90 samples (9 tissues from 5 old and 5 young mice) to explore effects of aging. Tissue-specific aging are presented here and we highlight the role of inflammation- and metabolism-related processes in white adipose tissue. We validated our approach through comparison with a global proteome survey across the tissues, work that we also provide as a general resource for the community.
HostingRepository	PRIDE
AnnounceDate	2020-04-27
AnnouncementXML	Submission_2020-04-26_23:31:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qing Yu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-04 08:38:19	ID requested
⏵ 1	2020-04-26 23:31:42	announced

Yu Q, Xiao H, Jedrychowski MP, Schweppe DK, Navarrete-Perea J, Knott J, Rogers J, Chouchani ET, Gygi SP, Sample multiplexing for targeted pathway proteomics in aging mice. Proc Natl Acad Sci U S A, 117(18):9723-9732(2020) [pubmed]

submitter keyword: targeted pathway proteomics, tissue-specific aging, isobaric labeling, real-time instrument control, Tomahto

Steven P Gygi
contact affiliation	Harvard medical school
contact email	steven_gygi@hms.harvard.edu
lab head
Qing Yu
contact affiliation	Harvard Medical School
contact email	qing_yu2@hms.harvard.edu
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/2020/04/PXD017385

PRIDE project URI

• PRIDE
  1. PXD017385
     1. Label: PRIDE project
     2. Name: Sample multiplexing for targeted pathway proteomics: application to aging mice