PXD003024

PXD003024 is an original dataset announced via ProteomeXchange.

Title	Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery
Description	Cerebrospinal fluid (CSF) is a body fluid of high clinical relevance and an important source of potential biomarkers for brain-associated damages such as traumatic brain injury, stroke, and for brain diseases like Alzheimer’s and Parkinson's . Herein, we have implemented, evaluated and validated a scalable automated proteomic pipeline (ASAP2) for the sample preparation and proteomic analysis of CSF, enabling increased throughput and robustness for biomarker discovery. Human CSF samples were depleted from abundant proteins, and submitted to automated reduction, alkylation, protein digestion, tandem mass tag (TMT) 6-plex labeling, pooling, and sample clean-up in a 96-well plate format before reversed-phase liquid chromatography tandem mass spectrometry (RP-LC MS/MS). First, we showed the impact on the CSF proteome coverage of applying the depletion of abundant proteins, which is usually performed on blood plasma or serum samples. Using ASAP2 to analyze 96 identical CSF samples, we determined the analytical figures of merit of our shotgun proteomic approach regarding proteome coverage consistency (i.e., 387 proteins), quantitative accuracy, and individual protein variability. We demonstrated that, as for human plasma samples, ASAP2 is efficient in analyzing large numbers of human CSF samples and is a valuable tool for biomarker discovery.
HostingRepository	PRIDE
AnnounceDate	2015-12-09
AnnouncementXML	Submission_2015-12-09_04:04:26.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	LOIC DAYON
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; TMT6plex-126 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-10-08 23:27:41	ID requested
1	2015-10-09 07:42:23	announced
2	2015-10-13 00:19:52	announced	Updated publication reference for PubMed record(s): 26452177.
⏵ 3	2015-12-09 04:04:28	announced	Updated publication details.

N, ú, ñ, ez Galindo A, Kussmann M, Dayon L, Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery. Anal Chem, 87(21):10755-61(2015) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: Automation, Brain, Clinical proteomics, Depletion, Isobaric labeling, Mass spectrometry, Tandem mass tags

Loïc Dayon
contact affiliation	Molecular Biomarkers Core, Nestlé Institute of Health Sciences, Lausanne, Switzerland
contact email	loic.dayon@rd.nestle.com
lab head
LOIC DAYON
contact affiliation	Nestlé Institute of Health Sciences SA
contact email	loic.dayon@rd.nestle.com
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/2015/12/PXD003024

PRIDE project URI

• PRIDE
  1. PXD003024
     1. Label: PRIDE project
     2. Name: Proteomics of Cerebrospinal Fluid: Throughput and Robustness Using a Scalable Automated Analysis Pipeline for Biomarker Discovery