PXD011076

PXD011076 is an original dataset announced via ProteomeXchange.

Title	Spiked human substantia nigra proteome data set for use as a spectral library for protein modelling and protein mapping
Description	This article describes a mass spectrometry data set generated from human substantia nigra tissue that was spiked with iRT peptides. The data set can be used as a spectral library for analysis of the human brain, especially human substantia nigra, for example, in the context of Parkinson’s disease. Obtaining a sufficient amount of high-quality substantia nigra tissue is the key limiting factor for establishing a brain region-specific spectral library. Hence, combining existing spectral libraries for data-independent acquisition analysis (DIA) can overcome this major limitation. Moreover, these data can be used to map brain region-specific proteins and to model brain region-specific pathways. Both can improve our understanding of the functioning of the brain in greater depth. In addition, these data can also be used to determine the optimal settings for measuring proteins and peptides of interest. To create the substantia nigra-specific spectral library, the tissue was first homogenized and then fractionated via different types of SDS gel electrophoresis, resulting in 18 fractions. These fractions were analysed in triplicate by nanoHPLC-ESI-MS/MS, resulting in 54 data files.
HostingRepository	PRIDE
AnnounceDate	2019-08-15
AnnouncementXML	Submission_2019-08-15_01:32:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Annika Guntermann
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-13 00:01:54	ID requested
⏵ 1	2019-08-15 01:40:22	announced

Steinbach S, Serschnitzki B, Gerlach M, Marcus K, May C, proteome data set for use as a spectral library for protein modelling and protein mapping. Data Brief, 23():103711(2019) [pubmed]

ProteomeXchange project tag: Human Brain Proteome Project (HUPO_HBPP) (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Biological

submitter keyword: substantia nigra, spectral library, protein modelling, DDA

Prof. Dr. Katrin Marcus
contact affiliation	Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
contact email	katrin.marcus@rub.de
lab head
Annika Guntermann
contact affiliation	Medizinisches Proteom-Center
contact email	Annika.Guntermann@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/2019/08/PXD011076

PRIDE project URI

• PRIDE
  1. PXD011076
     1. Label: PRIDE project
     2. Name: Spiked human substantia nigra proteome data set for use as a spectral library for protein modelling and protein mapping