PXD029891

PXD029891 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Benchmarking differential expression, imputation and quantification methods for proteomics data
Description	Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools including protein quantification, imputation, and differential expression (DE) analysis were generated in the past decade. However, searching optimized tools is still an unsolved issue. Moreover, due to the rapid development of RNA-Seq technology, a vast number of DE analysis methods are created. Applying these newly developed RNA-Seq-oriented tools to proteomics data is still a question that needs to be addressed. In order to benchmark these analysis methods, a proteomics dataset constituted the proteins derived from human, yeast, and drosophila with different ratios were generated. Based on this dataset, DE analysis tools (including array-based and RNA-Seq based), imputation algorithms, and protein quantification methods were compared and benchmarked. This study provided useful information on analyzing quantitative proteomics datasets. All the methods used in this study were integrated into Perseus which are available at https://www.maxquant.org/perseus.
HostingRepository	jPOST
AnnounceDate	2022-11-16
AnnouncementXML	Submission_2022-11-15_21:52:42.238.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miao-Hsia Lin
SpeciesList	scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-24 02:23:41	ID requested
⏵ 1	2022-11-15 21:52:44	announced

Publication List

Lin MH, Wu PS, Wong TH, Lin IY, Lin J, Cox J, Yu SH, Benchmarking differential expression, imputation and quantification methods for proteomics data. Brief Bioinform, 23(3):(2022) [pubmed]

Lin MH, Wu PS, Wong TH, Lin IY, Lin J, Cox J, Yu SH, Benchmarking differential expression, imputation and quantification methods for proteomics data. Brief Bioinform, 23(3):(2022) [pubmed]

Keyword List

submitter keyword: differential expression, proteomics, benchmark data, imputation, match between runs

submitter keyword: differential expression, proteomics, benchmark data, imputation, match between runs

Contact List

Miao-Hsia Lin
lab head
Miao-Hsia Lin
contact affiliation	Institute of Chemistry, Academia Sinica
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST 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://ftp.jpostdb.org/JPST001395/