PXD007529-1

PXD007529 is an original dataset announced via ProteomeXchange.

Title	Enrichment and quantitation of newly secreted proteins under serum condition by combining BONCAT and pulsed SILAC
Description	Despite the increasing interest of secretome involved in paracrine/autocrine mechanisms, the majority of the mass spectrometric cell secretome studies have been performed using serum-free medium (SFM), due to low-abundance of secreted proteins and high-abundance of contaminating fetal bovine serum (FBS) proteins in serum-containing medium (SCM). In this study, through the combination of bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed-SILAC (pSILAC), the low-abundant secreted proteins were captured selectively and quantified. We set up the combined BONCAT-pSILAC method by optimizing capturing condition and by using a composite human-FBS database, and applied it to the analysis of differentially secreted proteins between SFM and SCM. The amount of secreted proteins for 24 h in SCM was much bigger than that from SFM for U-87MG glioblastoma cells (1.28-fold) and mesenchymal stem cells from human umbilical cord blood (hUCB-MSCs; 2.01-fold). The proteins secreted more in SCM were predominantly predicted to be truly secretory. Therefore, this study suggests the analysis of the secretome should be processed in serum-containing medium that promotes cell proliferation and secretion.
HostingRepository	PRIDE
AnnounceDate	2019-03-13
AnnouncementXML	Submission_2019-03-12_21:20:32.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jihye Shin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-22 03:47:38	ID requested
⏵ 1	2019-03-12 21:20:33	announced
2	2024-10-22 03:59:50	announced	2024-10-22: Updated project metadata.

Shin J, Rhim J, Kwon Y, Choi SY, Shin S, Ha CW, Lee C, Comparative analysis of differentially secreted proteins in serum-free and serum-containing media by using BONCAT and pulsed SILAC. Sci Rep, 9(1):3096(2019) [pubmed]

curator keyword: Biological

submitter keyword: secretome, serum, FBS, BONCAT, pulsed SILAC, LC-MS/MS

Cheolju Lee
contact affiliation	Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Korea
contact email	jihye.shin.8406@gmail.com
lab head
Jihye Shin
contact affiliation	KIST
contact email	jihye.shin.8406@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD007529
     1. Label: PRIDE project
     2. Name: Enrichment and quantitation of newly secreted proteins under serum condition by combining BONCAT and pulsed SILAC