PXD004863

PXD004863 is an original dataset announced via ProteomeXchange.

Title	Expanding the cerebrospinal fluid endopeptidome
Description	Biomarkers of neurodegenerative disorders are needed to assist in diagnosis, to monitor disease progression and therapeutic interventions, and to provide insight into disease mechanisms. One route to identify such biomarkers is by proteomic and peptidomic analysis of cerebrospinal fluid (CSF). In the current study, we performed an in-depth analysis of the human CSF endopeptidome to establish an inventory that may serve as a basis for future targeted biomarker studies. High-pH reversed-phase HPLC was employed for peptide fractionation followed by low-pH nano-LC-MS analysis. Different software programs and scoring algorithms for peptide identification were employed and compared. A total of 18,031 endogenous peptides were identified (FDR = 1%), increasing the number of known CSF peptides 10-fold compared to previous studies. The peptides were derived from 2,053 proteins of which more than 60 have been linked to neurodegeneration. Notably, among the findings were six peptides derived from microtubule-associated protein tau, three of which span the diagnostically interesting threonine-181. Also, 213 peptides from amyloid precursor protein (APP), 58 of which were partially or completely within the sequence of amyloid β 1-40/42, as well as 109 peptides from apolipoprotein E, spanning sequences that discriminate between the E2/E3/E4 isoforms of the protein.
HostingRepository	PRIDE
AnnounceDate	2017-01-17
AnnouncementXML	Submission_2017-01-17_02:08:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Hansson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-18 02:22:31	ID requested
⏵ 1	2017-01-17 02:08:27	announced

Hansson KT, Skillb, ä, ck T, Pernevik E, Kern S, Portelius E, H, ö, glund K, Brinkmalm G, Holm, é, n-Larsson J, Blennow K, Zetterberg H, Gobom J, Expanding the cerebrospinal fluid endopeptidome. Proteomics, 17(5):(2017) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Cerebrospinal fluid, peptides, peptidomics, biomarkers, neurodegeneration, Alzheimer’s disease, Parkinson’s disease

Henrik Zetterberg
contact affiliation	- Inst. of Neuroscience and Physiology, Dept. of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden - Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden - Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
contact email	henrik.zetterberg@clinchem.gu.se
lab head
Karl Hansson
contact affiliation	Gothenburg University
contact email	karl.hansson@neuro.gu.se
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/2017/01/PXD004863

PRIDE project URI

• PRIDE
  1. PXD004863
     1. Label: PRIDE project
     2. Name: Expanding the cerebrospinal fluid endopeptidome