PXD008967-2

PXD008967 is an original dataset announced via ProteomeXchange.

Title	Surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) for enhanced proteomics
Description	As a popular sample preparation approach, Filter-aided sample preparation (FASP) has been widely used in proteomic analysis. However, several limitations have been noted, including sample loss during filtration, repetitive centrifugation steps, and the possibility of breakage of filtration membrane. Extraction bias among different sample preparation strategies is another challenging question. To overcome these limitations and address remaining challenges, we developed a novel surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) protocol. The new strategy resulted in higher protein yield, improved peptide recovery and protein coverage compared to two conventional sample preparation methods (FASP and urea). In combination of three strategies, more than 10,000 distinct protein groups were identified with 1% FDR from MDA-MB-231 cells without any pre-fractionation. This in-depth proteome analysis was accomplished by optimization of protein extraction, enzymatic digestion, LC gradient and peptide sequencing method. IPA analysis of protein exclusively identified in SCAD revealed several crucial signaling pathways which regulate breast cancer progression. An unbiased extraction of different categories of proteins associated with tumorigenesis was also demonstrated. This novel strategy not only expedites comprehensive protein identification but also post-translational modifications (PTMs) of proteins (e.g., glycosylation), thus is applicable for biomarker discovery in various types of cancers.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:42:57.699.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fengfei Ma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-16 02:39:41	ID requested
1	2018-10-19 12:42:06	announced
⏵ 2	2024-10-22 04:43:03	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.8b00197;

Ma F, Liu F, Xu W, Li L, Surfactant and Chaotropic Agent Assisted Sequential Extraction/On-Pellet Digestion (SCAD) for Enhanced Proteomics. J Proteome Res, 17(8):2744-2754(2018) [pubmed]

curator keyword: Technical

submitter keyword: Urea, protein digestion, protein detection,Protein extraction, peptide sequencing, LFQ, SCAD, iBAQ, FASP

Lingjun Li
contact affiliation	School of Pharmacy and Department of Chemistry University of Wisconsin-Madison
contact email	lingjun.li@wisc.edu
lab head
Fengfei Ma
contact affiliation	UW Madison
contact email	fma9@wisc.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/2018/10/PXD008967

PRIDE project URI

• PRIDE
  1. PXD008967
     1. Label: PRIDE project
     2. Name: Surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) for enhanced proteomics