PXD004824

PXD004824 is an original dataset announced via ProteomeXchange.

Title	DISMS2: A flexible algorithm for direct proteome-wide distance calculation of LC-MS/MS runs
Description	The classification of samples on a molecular level has manifold applications, from cancer biology, where the goal is to classify patients according to effective treatments, to phylogenetics to identify evolutionary relationships between species. In such scenarios modern molecular methods are based on the alignment of DNA or amino acid sequences, often only on selected parts of the genome, but also genome-wide comparisons of sequences are performed. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography - tandem mass spectrometry (LC-MS/MS). This technique is used to identify protein sequences from tandem mass spectra by means of database searches, given samples with known genome-wide sequence information, and then to apply sequence based methods. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without the need of database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:31:59.477.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laxmikanth Kollipara
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-16 23:56:12	ID requested
1	2017-03-13 04:00:27	announced
2	2017-10-02 07:59:27	announced	Updated publication reference for PubMed record(s): 28253837, 28959885.
⏵ 3	2024-10-22 04:32:09	announced	2024-10-22: Updated project metadata.

Rieder V, Blank-Landeshammer B, Stuhr M, Schell T, Bi, ß K, Kollipara L, Meyer A, Pfenninger M, Westphal H, Sickmann A, Rahnenf, ü, hrer J, DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics, 18(1):148(2017) [pubmed]

10.1021/acs.jproteome.7b00427;

Rieder V, Schork KU, Kerschke L, Blank-Landeshammer B, Sickmann A, Rahnenf, ü, hrer J, Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra. J Proteome Res, 16(11):4035-4044(2017) [pubmed]

10.1186/s12859-017-1514-2;

curator keyword: Technical

submitter keyword: Distance measurements, Spectral comparisions, LC-MS/MS

Albert Sickmann
contact affiliation	Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Otto-Hahn-Straße 6b 44227 Dortmund, Germany
contact email	sickmann@isas.de
lab head
Laxmikanth Kollipara
contact affiliation	Leibniz – Institut für Analytische Wissenschaften - ISAS - e.V.
contact email	laxmikanth.kollipara@isas.de
dataset submitter

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.pride.ebi.ac.uk/pride/data/archive/2017/03/PXD004824

PRIDE project URI

• PRIDE
  1. PXD004824
     1. Label: PRIDE project
     2. Name: DISMS2: A flexible algorithm for direct proteome-wide distance calculation of LC-MS/MS runs