PXD012987-1

PXD012987 is an original dataset announced via ProteomeXchange.

Title	Reproducibility, specificity and accuracy of DIA quantification - Spectral Libraries
Description	For the complete description see the manuscript. Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analysis is the availability of spectral libraries for the peptide identification and quantification. Several researches were already conducted regarding the creation of spectral libraries from DDA analyses and obtaining identifications with these in DIA measurements. But so far only few experiments were conducted, to estimate the effect of these libraries on the quantitative level. In this work we created a spike-in gold standard dataset with known contents and ratios of proteins in a complex sample matrix. With this dataset, we first created spectral libraries using different sample preparation approaches with and without sample prefractionation on peptide and protein level. Two different search engines were used for protein identification. In total, five different spike-in states were compared with DIA analyses, comparing eight different spectral libraries generated by varying approaches and one library free method, as well as one default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding analyses was inspected, but also the number of expected and identified significant quantifications and their ratios were thoroughly examined.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:40:07.350.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD012987
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Julian Uszkoreit
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	Ammonia-loss; Deamidated; Ammonium; Oxidation; Carbamidomethyl; Gln->pyro-Glu
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-05 23:48:31	ID requested
⏵ 1	2024-10-08 11:40:08	announced

10.6019/PXD012987;

Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Eisenacher M, Marcus K, Uszkoreit J, Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition. Mol Cell Proteomics, 19(1):181-197(2020) [pubmed]

10.1074/mcp.ra119.001714;

curator keyword: Technical

submitter keyword: DIA, label-free quantification, peptide identification, spectral library,data-independent acquisition

Katrin Marcus
contact affiliation	Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
contact email	katrin.marcus@rub.de
lab head
Julian Uszkoreit
contact affiliation	Ruhr-Universität Bochum, Medical Faculty, Medizinisches Proteom-Center, Medical Bioinformatics / Functional Proteomics
contact email	julian.uszkoreit@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/2019/11/PXD012987

PRIDE project URI

• PRIDE
  1. PXD012987
     1. Label: PRIDE project
     2. Name: Reproducibility, specificity and accuracy of DIA quantification - Spectral Libraries