PXD010698

PXD010698 is an original dataset announced via ProteomeXchange.

Title	Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry
Description	Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF (n=5) CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) applying to CSF DIA of three replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 minute gradient. Compared to a conventional DDA method, our DIA approach both increased the number of identified protein groups with 1574 compared to DDA with 648 over 50 % with a comprehensive spectral library (generated with DDA measurements from five native CSF and 54 substantia nigra fractions) and decreased the coefficient of variation to 6 %, compared to 11 % with a DDA method. We also could show that a sample specific spectral library generated only from native CSF increased the identification reproducibility from three DIA replicates to 90 % (77 % with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA over 60 brain-originated proteins could be identified compared to only eleven with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF.
HostingRepository	PRIDE
AnnounceDate	2018-09-17
AnnouncementXML	Submission_2018-09-17_00:29:41.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD010698
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Katalin Barkovits
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	residues isobaric at 128.058578 Da; Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-06 06:25:41	ID requested
⏵ 1	2018-09-17 00:29:42	announced

Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K, Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry. J Proteome Res, 17(10):3418-3430(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: proteomics, data-independent acquisition mass spectrometry, DIA, cerebrospinal fluid, CSF, spectral library

Katrin Marcus
contact affiliation	Katrin Marcus Medizinisches Proteom-Center Ruhr-Universität Bochum Zentrum für klinische Forschung (ZKF) Raum 1.055 Universitätsstraße 150 44801 Bochum Germany
contact email	Katrin.marcus@rub.de
lab head
Katalin Barkovits
contact affiliation	Ruhr University Bochum
contact email	katalin.barkovits@rub.de
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/2018/09/PXD010698

PRIDE project URI

• PRIDE
  1. PXD010698
     1. Label: PRIDE project
     2. Name: Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry