PXD001180-2

PXD001180 is an original dataset announced via ProteomeXchange.

Title	Human brain phosphoproteome analyzed by refined phosphopeptide enrichment and high resolution LC-MS/MS
Description	Alzheimer’s disease (AD) is the most common form of dementia, characterized by progressive loss of cognitive function. One of the pathological hallmarks of AD is the formation of neurofibrillary tangles composed of abnormally hyperphosphorylated tau protein, but global deregulation of protein phosphorylation in AD is not well analyzed. Here we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a non-phosphopeptide competitor to reduce background. The procedure was further tuned with respect to peptide-to-bead ratio, phosphopeptide recovery and purity. Using this refined method and 9 h LC-MS/MS, we analyzed phosphoproteome in one milligram of digested AD brain lysate, identifying 5,243 phosphopeptides containing 3,717 non-redundant phosphorylation sites on 1,455 proteins. This modified enrichment method is simple and highly efficient. The AD case study demonstrates its feasibility of dissecting phosphoproteome in a limited amount of postmortem human brain.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:06:40.537.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	xusheng wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2014-07-28 23:53:17	ID requested
1	2015-02-02 05:03:38	announced
⏵ 2	2024-10-22 04:06:41	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201400171;

Tan H, Wu Z, Wang H, Bai B, Li Y, Wang X, Zhai B, Beach TG, Peng J, Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome. Proteomics, 15(2-3):500-7(2015) [pubmed]

curator keyword: Biological

submitter keyword: Phosphorylation, human brain, Alzheimer's disease, phosphopeptide enrichment, LC-MS/MS

Junmin Peng
contact affiliation	St. Jude Children's Research Hospital
contact email	junmin.peng@stjude.org
lab head
xusheng wang
contact affiliation	St. Jude Children's research hospital
contact email	xusheng.wang@stjude.org
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/2015/01/PXD001180

PRIDE project URI

• PRIDE
  1. PXD001180
     1. Label: PRIDE project
     2. Name: Human brain phosphoproteome analyzed by refined phosphopeptide enrichment and high resolution LC-MS/MS