PXD037650

PXD037650 is an original dataset announced via ProteomeXchange.

Title	Quality control in quantitative proteomics: a case study for the human CSF proteome
Description	Proteome studies using mass spectrometry (MS)-based quantification is a main approach for the discovery of new biomarkers. However, a number of analytical conditions in front and during MS data acquisition can affect the accuracy of the obtained outcome. Therefore, comprehensive quality assessment of the acquired data plays a central role in quantitative proteomics, though due to immense complexity of MS data it is often neglected. Here, we practically address the quality assessment of quantitative MS data describing key steps for the evaluation including the levels: raw data, identification and quantification. With this, four independent datasets from cerebrospinal fluid, an important biofluid for neurodegenerative diseases biomarker studies, were assessed demonstrating that already sample processing-based differences are reflected on all three levels but with a varying impact on the quality of the quantitative data.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:49.646.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD037650
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Svitlana Rozanova
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 00:55:45	ID requested
1	2023-04-12 02:04:39	announced
⏵ 2	2023-11-14 08:44:50	announced	2023-11-14: Updated project metadata.

10.6019/PXD037650;

Rozanova S, Uszkoreit J, Schork K, Serschnitzki B, Eisenacher M, T, ö, nges L, Barkovits-Boeddinghaus K, Marcus K, Quality Control-A Stepchild in Quantitative Proteomics: A Case Study for the Human CSF Proteome. Biomolecules, 13(3):(2023) [pubmed]

submitter keyword: cerebrospinal fluid, in-solution digestion, proteomics, quality control,mass spectrometry, label-free quantification, FASP

Prof. Katrin Marcus
contact affiliation	Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, Bochum Germany Ruhr University Bochum, Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Bochum, Germany
contact email	Katrin.Marcus@rub.de
lab head
Svitlana Rozanova
contact affiliation	Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center
contact email	Svitlana.Rozanova@ruhr-uni-bochum.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/2023/04/PXD037650

PRIDE project URI

• PRIDE
  1. PXD037650
     1. Label: PRIDE project
     2. Name: Quality control in quantitative proteomics: a case study for the human CSF proteome