PXD057850

PXD057850 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms
Description	Stable isotopic labeling by amino acids in cell culture (SILAC) is a powerful metabolic labeling technique with widespread applications and diverse study designs. SILAC proteomics requires the confident identification and quantification of complete isotopic versions of proteins and peptides during data acquisition and analysis. However, different SILAC workflows and data analysis platforms have not been comparatively evaluated. To fill this critical gap and provide practical user guidelines for SILAC proteomics data analysis, we designed a comprehensive benchmarking pipeline to evaluate different SILAC workflows and commonly used data analysis software. Ten different data analysis platforms were evaluated for static and dynamic SILAC labeling with both DDA and DIA methods. Both in-house generated and repository SILAC proteomics datasets were used for benchmarking with hundreds of raw data files from HeLa and neuron samples. We evaluated twelve performance metrics for SILAC proteomics including identification, quantification, accuracy, precision, reproducibility, filtering criteria, missing values, false discovery rate, protein half-life measurement, completeness, unique software features, and speed of data analysis. In summary, this study provided the first systematic evaluation of different SILAC data analysis platforms with practical guidelines to assist decision-making in SILAC proteomics study design and data analysis.
HostingRepository	MassIVE
AnnounceDate	2024-11-19
AnnouncementXML	Submission_2024-11-19_08:12:48.631.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ling Hao
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl; Acetyl
Instrument	Q Exactive HF-X

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-13 08:44:00	ID requested
⏵ 1	2024-11-19 08:12:49	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Dynamic SILAC, Neuron, pulse SILAC, dSILAC, pSILAC, Turnover, Arg10, Lys8, DatasetType:Proteomics

submitter keyword: Dynamic SILAC, Neuron, pulse SILAC, dSILAC, pSILAC, Turnover, Arg10, Lys8, DatasetType:Proteomics

Contact List

Ling Hao
contact affiliation	University of Maryland
contact email	haolab.19@gmail.com
lab head
Ling Hao
contact affiliation	University of Maryland
contact email	haolab.19@gmail.com
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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://massive.ucsd.edu/v07/MSV000096401/

MassIVE dataset URI

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://massive.ucsd.edu/v07/MSV000096401/