PXD015189

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]

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

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/

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/