PXD012520

PXD012520 is an original dataset announced via ProteomeXchange.

Title	Evosep One Enables Robust Quantitative Deep Proteome Coverage using Tandem Mass Tags while Significantly Reducing Machine Time
Description	The balance between comprehensively analyzing the proteome and using valuable mass spectrometry time is a genuine challenge in the field of proteomics. Multidimensional fractionation strategies have significantly increased proteome coverage, but often at the cost of increased mass analysis time, despite advances in mass spectrometer acquisition rates. Recently, the Evosep One liquid chromatography system was shown to analyze peptide samples in a high throughput manner without sacrificing in depth proteomics coverage. We demonstrate incorporation of Evosep One technology into our multiplexing workflow for quantitative analysis of tandem mass tag (TMT)-labeled non-small cell lung carcinoma (NSCLC) patient-derived xenografts (PDXs). Using a 30 samples per day Evosep workflow, >12,000 proteins were identified in 48 hours of mass spectrometry time, which is comparable to the number of proteins identified by our conventional concatenated EASY-nLC workflow in 67.5 hours. Shorter Evosep gradient lengths reduced the number of protein identifications by 10%, while decreasing mass analysis time by 50%. Thus, our Evosep workflow enables quantitative analysis of multiplexed samples in less time without conceding depth of proteome coverage.
HostingRepository	PRIDE
AnnounceDate	2019-04-04
AnnouncementXML	Submission_2019-04-04_00:57:24.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD012520
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jonathan Krieger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Deamidated; TMT6plex; Oxidation; Acetyl; Carbamidomethyl
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-28 01:12:27	ID requested
⏵ 1	2019-04-04 00:57:27	announced

Krieger JR, Wybenga-Groot LE, Tong J, Bache N, Tsao MS, Moran MF, Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time. J Proteome Res, 18(5):2346-2353(2019) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: Evosep, LC-MS/MS, TMT, mass analysis time, nonsmall cell lung carcinoma (NSCLC) patient-derived xenografts (PDX)

Michal F. Moran
contact affiliation	SPARC Biocentre, The Hospital for Sick Children, Program in Cell Biology, The Hospital for Sick Children, Department of Medical Biophysics, University of Toronto.
contact email	m.moran@utoronto.ca
lab head
Jonathan Krieger
contact affiliation	SickKids/University of Toronto
contact email	Jonathan.krieger@sickkids.ca
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/2019/04/PXD012520

PRIDE project URI

• PRIDE
  1. PXD012520
     1. Label: PRIDE project
     2. Name: Evosep One Enables Robust Quantitative Deep Proteome Coverage using Tandem Mass Tags while Significantly Reducing Machine Time