PXD020806-1

PXD020806 is an original dataset announced via ProteomeXchange.

Title	Isobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)
Description	A vast assortment of human cell lines is available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, we determined the relative protein abundance profiles of a panel of eight diverse, but commonly studied, human cell lines. This panel includes: HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. We use a mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth. To this end, our strategy leverages TMTpro16-based sample multiplexing, high-Field Asymmetric Ion Mobility Spectrometry (FAIMS), and real-time database searching (RTS). The data show that cell line diversity was reflective of differences in the relative protein abundance profiles. We also determined that several hundred proteins were highly enriched for a given cell line and performed gene ontology and pathway analysis on these cell line-enriched proteins. We provide an R Shiny application to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection in addressing a given scientific inquiry or in improving an experimental design.
HostingRepository	PRIDE
AnnounceDate	2020-10-19
AnnouncementXML	Submission_2020-10-19_00:13:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-08 16:59:37	ID requested
⏵ 1	2020-10-19 00:13:39	announced

Liu X, Gygi SP, Paulo JA, Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching. Proteomics, 21(1):e2000218(2021) [pubmed]

submitter keyword: SPS-MS3, Multi-Notch, TMTpro, Eclipse, RTS, FAIMS

Joao A. Paulo
contact affiliation	Department of Cell Biology, Harvard Medical School, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.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/2020/10/PXD020806

PRIDE project URI

• PRIDE
  1. PXD020806
     1. Label: PRIDE project
     2. Name: Isobaric tag-based protein profiling across eight human cell lines using high-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and real-time database searching (RTS)