PXD020807

PXD020807 is an original dataset announced via ProteomeXchange.

Title	Temporal proteomic profiling of SH-SY5Y differentiation with retinoic acid using a FAIMS and Real-Time Searching strategy
Description	The SH-SY5Y cell line is often used as a surrogate for neurons in cell-based studies. This cell line is frequently differentiated with all-trans retinoic acid (ATRA) over a 7-day period which confers neuron-like properties to the cells. However, no analysis of proteome remodeling has followed the progress of this transition. Here, we quantitatively profiled over 9,400 proteins across a 7-day treatment with retinoic acid using state-of-the-art mass spectrometry-based proteomics technologies, including FAIMS, real-time database searching, and TMTpro16 sample multiplexing. Gene ontology analysis revealed that categories with the highest increases in abundance were related to the plasma membrane/extracellular space. To showcase our dataset, we surveyed the protein abundance profiles linked to neurofilament bundle assembly, neuron projections, and neuronal cell body formation. These proteins exhibited increases in abundance level, yet we observed multiple patterns among the queried proteins. The data presented represent a rich resource for investigating temporal protein abundance changes in SH-SY5Y cells differentiated with retinoic acid. Moreover, the sample preparation and data acquisition strategies used here can be readily applied to any analogous cell line differentiation analysis.
HostingRepository	PRIDE
AnnounceDate	2020-10-20
AnnouncementXML	Submission_2020-10-20_07:13:39.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 Fusion Lumos; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-08 17:00:02	ID requested
⏵ 1	2020-10-20 07:13:40	announced

Zhang T, Gygi SP, Paulo JA, Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching. J Proteome Res, 20(1):704-714(2021) [pubmed]

submitter keyword: SPS-MS3, Multi-Notch, TMTpro, Eclipse, ATRA, retinoic acid

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/PXD020807

PRIDE project URI

• PRIDE
  1. PXD020807
     1. Label: PRIDE project
     2. Name: Temporal proteomic profiling of SH-SY5Y differentiation with retinoic acid using a FAIMS and Real-Time Searching strategy