PXD029891-1
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] |
Keyword List
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 |
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/ |