PXD036134-2

PXD036134 is an original dataset announced via ProteomeXchange.

Title	MS-DAP platform for label-free proteomics uncovers optimal workflows in benchmark datasets and increased sensitivity in analysis of Alzheimer's biomarker data
Description	In the rapidly moving proteomics field, a diverse patchwork of algorithms for data normalization and differential expression analysis is used by the community. We generated an all-inclusive mass spectrometry downstream analysis pipeline (MS-DAP) that integrates many algorithms for normalization and statistical analyses and produces standardized quality reporting with extensive data visualizations. Second, systematic evaluation of normalization and statistical algorithms on various benchmarking datasets, including additional data generated in this study, suggest best-practices for data analysis. Commonly used approaches for differential testing based on moderated t-statistics are consistently outperformed by more recent statistical models, all integrated in MS-DAP, and we encourage their adoption. Third, we introduced a novel normalization algorithm that rescues deficiencies observed in commonly used normalization methods. Finally, we used the MS-DAP platform to re-analyze a recently published large-scale proteomics dataset of CSF from AD patients. This revealed increased sensitivity, resulting in additional significant target proteins which improved overlap with results reported in related studies and includes a large set of new potential AD biomarkers in addition to previously reported.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:02:36.329.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frank Koopmans
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-17 00:57:04	ID requested
1	2023-03-10 15:21:51	announced
⏵ 2	2023-11-14 08:02:37	announced	2023-11-14: Updated project metadata.

Koopmans F, Li KW, Klaassen RV, Smit AB, MS-DAP Platform for Downstream Data Analysis of Label-Free Proteomics Uncovers Optimal Workflows in Benchmark Data Sets and Increased Sensitivity in Analysis of Alzheimer's Biomarker Data. J Proteome Res, 22(2):374-386(2023) [pubmed]

submitter keyword: Alzheimer’s disease,proteomics, software, benchmarking, bioinformatics

August B. Smit
contact affiliation	Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands.
contact email	guus.smit@vu.nl
lab head
Frank Koopmans
contact affiliation	VU University
contact email	frank.koopmans@vu.nl
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/2023/03/PXD036134

PRIDE project URI

• PRIDE
  1. PXD036134
     1. Label: PRIDE project
     2. Name: MS-DAP platform for label-free proteomics uncovers optimal workflows in benchmark datasets and increased sensitivity in analysis of Alzheimer's biomarker data