PXD018247-1

PXD018247 is an original dataset announced via ProteomeXchange.

Title	NanoTPOT: Enhanced Sample Preparation for Quantitative Na-noproteomic Analysis (revision work)
Description	With the ever-growing need for protein-level understanding in pathological research, proteomics researchers thrive to exam-ine detailed proteome dynamics using crucial, yet often limited, primary and clinical samples. Aside from mass spectrometer instrumentation advancement, a single-tube-based high-throughput sample processing workflow is imperative to ensure sen-sitive, quantitative and reproducible protein analysis for these increasingly sophisticated studies. Leveraging the benefits of an acid-cleavable detergent, RapiGest SF Surfactant (Waters Corporation), we developed and optimized a nanoproteomic workflow that we termed Nanogram TMT Processing in One Tube (NanoTPOT). Through the assessment of proteolytic di-gestion, tandem mass tag (TMT) labeling, online and offline fractionation strategies, our optimized workflow effectively eliminated the need for sample desalting and enabled compatible sample processing for mass spectrometry analysis. We further applied the NanoTPOT workflow to examine cellular response to stress caused by dithiothreitol in HeLa cells, where we identified and quantified 6935 and 5474 proteins in TMT 10-plex experiments with one microgram of lysate protein and 2000 sorted HeLa cells (500ng lysate protein) in each channel, respectively. Our workflow has been proven to be an effec-tive alternative for current nanoproteomic sample processing to minimize sample loss in biological and clinical applications.
HostingRepository	PRIDE
AnnounceDate	2021-03-16
AnnouncementXML	Submission_2021-03-16_06:43:22.693.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yu Lu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-30 00:20:40	ID requested
⏵ 1	2021-03-16 06:43:23	announced

Wu R, Pai A, Liu L, Xing S, Lu Y, NanoTPOT: Enhanced Sample Preparation for Quantitative Nanoproteomic Analysis. Anal Chem, 92(9):6235-6240(2020) [pubmed]

submitter keyword: Hela, TMT

Yu Lu
contact affiliation	Department of Biochemistry and Biomedical Sciences McMaster University
contact email	yu.lu@mcmaster.ca
lab head
Yu Lu
contact affiliation	McMaster University
contact email	yu.lu@mcmaster.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/2021/03/PXD018247

PRIDE project URI

• PRIDE
  1. PXD018247
     1. Label: PRIDE project
     2. Name: NanoTPOT: Enhanced Sample Preparation for Quantitative Na-noproteomic Analysis (revision work)