PXD010587

PXD010587 is an original dataset announced via ProteomeXchange.

Title	MS2-Deisotoper: A tool for deisotoping high-resolution MS/MS spectra in normal and heavy isotope-labelled samples
Description	High-resolution MS/MS spectra of peptides can be deisotoped to identify monoisotopic masses of peptide fragments. The use of such masses should improve protein identification rates. However, deisotoping is not universally used and its benefits have not been fully explored. Here, we developed MS2-Deisotoper, a tool for use prior to database search, to identify monoisotopic peaks in centroided MS/MS spectra. MS2-Deisotoper works by comparing the mass and relative intensity of each peptide fragment peak to every other peak of greater mass, and by applying a set of rules concerning mass and intensity differences. After comprehensive parameter optimisation, we show that MS2-Deisotoper could improve the number of peptide spectrum matches (PSMs) identified by up to 8.2% and proteins by up to 2.8%. It was effective with SILAC and non-SILAC MS/MS data. The identification of unique peptide sequences was also improved, increasing the number of human proteoforms by 3.7%. Detailed investigation of results showed that deisotoping increases Mascot ion scores, improves FDR estimation for PSMs and leads to greater protein sequence coverage. At a peptide level, we found that the efficacy of deisotoping was affected by peptide mass and charge. MS2-Deisotoper can be used via a user interface or as a command-line tool.
HostingRepository	PRIDE
AnnounceDate	2019-08-05
AnnouncementXML	Submission_2019-08-05_02:14:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aidan Tay
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	6x(13)C labeled residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2018-07-27 01:35:43	ID requested
⏵ 1	2019-08-05 02:14:37	announced

Tay AP, Liang A, Hamey JJ, Hart-Smith G, Wilkins MR, MS2-Deisotoper: A Tool for Deisotoping High-Resolution MS/MS Spectra in Normal and Heavy Isotope-Labelled Samples. Proteomics, 19(17):e1800444(2019) [pubmed]

submitter keyword: deisotoping, monoisotopic mass, protein identification, proteomic software, tandem mass spectrometry, SILAC

Marc Ronald Wilkins
contact affiliation	Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
contact email	m.wilkins@unsw.edu.au
lab head
Aidan Tay
contact affiliation	University of New South Wales
contact email	a.tay@unswalumni.com
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/2019/08/PXD010587

PRIDE project URI

• PRIDE
  1. PXD010587
     1. Label: PRIDE project
     2. Name: MS2-Deisotoper: A tool for deisotoping high-resolution MS/MS spectra in normal and heavy isotope-labelled samples