PXD015189-2
PXD015189 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Peak identification and quantification by proteomic mass spectrogram decomposition |
Description | Recent advances in liquid chromatography/mass spectrometry (LC/MS) technology have improved the sensitivity, resolution, and speed of proteome analysis, resulting in demand for sophisticated algorithms to interpret complex mass spectrograms. Here, we propose a novel statistical method, proteomic mass spectrogram decomposition (ProtMSD), for joint identification and quantification of peptides and proteins. Given the proteomic mass spectrogram and the reference mass spectra of possible peptide ions associated with proteins from selected run or runs as a dictionary, ProtMSD estimates the chromatograms of those peptide ions, under a group sparsity constraint without using the conventional careful pre-processing (e.g., thresholding and peak picking). We show that the method was significantly improved by using protein-peptide hierarchical relationships, isotopic distribution profiles, reference retention times of peptide ions, and pre-learned mass spectra of noise. We examined the concept of database search, library search, and match-between-runs. This is the first attempt to use a matrix decomposition technique as a tool for LC/MS-based proteome identification and quantification. |
HostingRepository | jPOST |
AnnounceDate | 2021-03-06 |
AnnouncementXML | Submission_2022-09-18_04:07:33.763.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Pasrawin Taechawattananant |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; unknown modification |
Instrument | Q Exactive; LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2019-08-27 19:13:11 | ID requested | |
1 | 2021-03-05 07:00:07 | announced | |
⏵ 2 | 2022-09-18 04:07:34 | announced | 2022-09-18: Updated FTP location. |
Publication List
Taechawattananant P, Yoshii K, Ishihama Y, Peak Identification and Quantification by Proteomic Mass Spectrogram Decomposition. J Proteome Res, 20(5):2291-2298(2021) [pubmed] |
Keyword List
submitter keyword: bioinformatics, machine learning, mass spectrogram, match-between-runs, matrix decomposition, protein identification and quantification, shotgun proteomics |
Contact List
Yasushi Ishihama | |
---|---|
lab head | |
Pasrawin Taechawattananant | |
contact affiliation | Kyoto University |
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/JPST000663/ |