PXD003308-1

PXD003308 is an original dataset announced via ProteomeXchange.

Title	Half decimal place rule .
Description	Many MS2 spectra in bottom-up proteomics experiments remain unassigned. To improve proteome coverage, we applied the half decimal place rule (HDPR) to remove non-peptidic molecules. The HDPR considers the ratio of the first digit after the decimal point to the full molecular mass and results in a relatively small permitted mass window for most peptides. Although the HDPR has been described previously, it has never been integrated into an acquisition strategy using high resolution mass spectrometers. The HDPR was applied to three technical replicates of an in-solution tryptic digest of HeLa cells which were analysed by LC-MS using a Q Exactive mass spectrometer.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_10:03:11.368.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Koehler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-09 01:44:34	ID requested
⏵ 1	2024-10-07 10:03:12	announced

10.1002/rcm.7780;

Koehler CJ, Bollineni RC, Thiede B, Application of the half decimal place rule to increase the peptide identification rate. Rapid Commun Mass Spectrom, 31(2):227-233(2017) [pubmed]

curator keyword: Technical

submitter keyword: Human, LC-MSMS, mass defect, HDPR, DDA

Bernd Thiede
contact affiliation	Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
contact email	bernd.thiede@ibv.uio.no
lab head
Christian Koehler
contact affiliation	University of Oslo
contact email	christian.koehler@ibv.uio.no
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/2022/02/PXD003308

PRIDE project URI

• PRIDE
  1. PXD003308
     1. Label: PRIDE project
     2. Name: Half decimal place rule