PXD022891

PXD022891 is an original dataset announced via ProteomeXchange.

Title	Automated 16plex plasma proteomics with real-time search and ion mobility mass spectrometry enables large scale profiling in naked mole-rats and mice.
Description	Performing large-scale plasma proteome profiling is challenging due to limitations imposed by lengthy preparation and instrument time. We present a fully Automated Multiplexed Proteome Profiling Platform (AutoMP3) using the Hamilton VantageTM liquid handling robot capable of preparing hundreds to thousands of samples. To maximize protein depth in single shot runs we combined 16plex Tandem Mass Tags (TMTpro) with high-field asymmetric waveform ion mobility spectrometry (FAIMS Pro) and real-time search (RTS). We quantified over 40 proteins / min / sample, doubling the previously published rates. We applied AutoMP3 to investigate the naked mole-rat plasma proteome both as a function of circadian cycle and in response to ultraviolet (UV) treatment. In keeping with the lack of synchronized circadian rhythms in naked mole-rats, we find few circadian patterns in plasma proteins over the course of 48hr. Furthermore, we quantify many disparate changes between mice and naked mole-rats at both 48hr and one week after UV exposure. These species differences in plasma protein temporal responses could contribute to the pronounced cancer resistance observed in naked mole-rats.
HostingRepository	PRIDE
AnnounceDate	2021-02-04
AnnouncementXML	Submission_2021-02-04_00:53:47.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sasha Gaun
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Heterocephalus glaber; NCBI TaxID: 10181;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-03 03:17:48	ID requested
⏵ 1	2021-02-04 00:53:48	announced

Gaun A, Lewis Hardell KN, Olsson N, O'Brien JJ, Gollapudi S, Smith M, McAlister G, Huguet R, Keyser R, Buffenstein R, McAllister FE, Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice. J Proteome Res, 20(2):1280-1295(2021) [pubmed]

submitter keyword: Mouse and Naked-Mole Rat Plasma

Fiona E. McAllister
contact affiliation	Calico Labs, United States
contact email	fiona@calicolabs.com
lab head
Sasha Gaun
contact affiliation	Calico Labs
contact email	aleksandergaun@gmail.com
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/2021/02/PXD022891

PRIDE project URI

• PRIDE
  1. PXD022891
     1. Label: PRIDE project
     2. Name: Automated 16plex plasma proteomics with real-time search and ion mobility mass spectrometry enables large scale profiling in naked mole-rats and mice.