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dc.contributor.authorSmith, Tom
dc.contributor.authorAndrejeva, Anna
dc.contributor.authorChristopher, Josie
dc.contributor.authorCrook, Oliver
dc.contributor.authorElzek, Mohammed
dc.contributor.authorLilley, Kathryn
dc.date.accessioned2021-11-10T00:31:11Z
dc.date.available2021-11-10T00:31:11Z
dc.date.issued2021-11-08
dc.identifier.issn2694-250X
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/330532
dc.description.abstractTandem 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 in version 3 of the instrument acquisition software, Tune. However, 53 % of Orbitrap Fusion, Lumos or Eclipse submissions to PRIDE were generated using prior software versions. To quantify the impact of the notch on existing quantitative proteomics data, we generated a mixed species benchmark and acquired quantitative data using Tune versions 2 and 3. Sub-notch intensities are predominantly underestimated with Tune version 2, leading to overestimation 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. 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 a typical proteomics experiment.
dc.publisherAmerican Chemical Society
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titlePrior Signal Acquisition Software Versions for Orbitrap Underestimate Low Isobaric Mass Tag Intensities, Without Detriment to Differential Abundance Experiments
dc.typeArticle
prism.publicationDate2021
prism.publicationNameACS Measurement Science Au
dc.identifier.doi10.17863/CAM.77975
dcterms.dateAccepted2021-11-08
rioxxterms.versionofrecord10.1021/acsmeasuresciau.1c00053
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2021-11-08
dc.contributor.orcidSmith, Tom [0000-0002-0697-8777]
dc.contributor.orcidChristopher, Josie [0000-0001-7077-4894]
dc.contributor.orcidLilley, Kathryn [0000-0003-0594-6543]
dc.identifier.eissn2694-250X
rioxxterms.typeJournal Article/Review
pubs.funder-project-idWellcome Trust (110170/Z/15/Z)
pubs.funder-project-idBiotechnology and Biological Sciences Research Council (BB/R505304/1)
pubs.funder-project-idWellcome Trust (110071/Z/15/Z)
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) Research Infrastructures (RI) (823839)
cam.issuedOnline2022-03-09
datacite.issupplementedby.doi10.5281/zenodo.5519228
cam.orpheus.success2021-11-09 - Embargo set during processing via Fast-track


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International