PXD027248-1

PXD027248 is an original dataset announced via ProteomeXchange.

Title	Prior Signal Acquisition Software Versions For Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments
Description	Tandem mass tags (TMT) enable simple and accurate quantitative proteomics for multiplexed samples by relative quantification of tag reporter ions. Orbitrap™ quantification of reporter ions has been associated with a characteristic notch region in intensity distribution, within which few reporter intensities are recorded. This has been resolved with updated instrument acquisition software, however, 53 % of Orbitrap submissions to PRIDE were generated using the prior software versions. To quantify the impact of the notch on existing quantitative proteomics data, we generate a mixed species benchmark and acquired quantitative data using the outdated software version. Sub-notch intensities are systemically underestimated, leading to over-estimation of the true differences in intensities between samples. However, when summarising reporter ion intensities to higher level features, such as peptides and proteins, few features are significantly affected. The analysis of benchmark dataset indicates that the targeted removal of spectra with reporter ion intensities below the notch is not beneficial for differential peptide or protein testing. Overall, we find the systematic quantification bias associated with the notch is not detrimental for typical proteomics experiments
HostingRepository	PRIDE
AnnounceDate	2021-07-20
AnnouncementXML	Submission_2021-07-20_04:26:29.961.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rayner Queiroz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-12 08:17:44	ID requested
⏵ 1	2021-07-20 04:26:30	announced

Dataset with its publication pending

submitter keyword: TMT, Orbitrap, Tune, Notch

Professor Kathryn Lilley
contact affiliation	Department of Biochemistry, University of Cambridge, UK
contact email	ksl23@cam.ac.uk
lab head
Rayner Queiroz
contact affiliation	University of Cambridge
contact email	rq214@cam.ac.uk
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/2021/07/PXD027248

PRIDE project URI

• PRIDE
  1. PXD027248
     1. Label: PRIDE project
     2. Name: Prior Signal Acquisition Software Versions For Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments