PXD017778

PXD017778 is an original dataset announced via ProteomeXchange.

Title	Triggered offset fragmentation allows massively multiplexed target profiling on quadrupole-orbitrap mass spectrometers
Description	Parallel reaction monitoring (PRM) on quadrupole-orbitrap mass spectrometers has a limited multiplexing capacity which depends heavily on the reproducibility of peptide retention times. To overcome these limitations, we aimed to establish a data acquisition mode that allows retention-time-independent massive multiplexing on quadrupole-orbitrap mass spectrometers. The presented method is based on data-dependent acquisition and is called pseudo-PRM. In principle, high-intensity stable isotope-labeled peptides are used to trigger the repeated fragmentation of the corresponding light peptides. In this way, pseudo-PRM data can be analyzed like normal PRM data with Skyline. We tested pseudo-PRM for the target detection from yeast, human cells, and serum, and assessed the quantification accuracy/precision and sensitivity. Moreover, we analyzed multiplexing of more than 1,000 targets in a single pseudo-PRM run. Finally, we applied pseudo-PRM to quantify vaccinia virus proteins during infection, verifying that pseudo-PRM presents an alternative method for multiplexed target profiling on quadrupole-orbitrap mass spectrometers.
HostingRepository	PRIDE
AnnounceDate	2020-06-19
AnnouncementXML	Submission_2020-06-19_01:24:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joerg Doellinger
SpeciesList	scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-28 03:43:33	ID requested
⏵ 1	2020-06-19 01:24:38	announced

Grossegesse M, Hartkopf F, Nitsche A, Doellinger J, Stable Isotope-Triggered Offset Fragmentation Allows Massively Multiplexed Target Profiling on Quadrupole-Orbitrap Mass Spectrometers. J Proteome Res, 19(7):2854-2862(2020) [pubmed]

submitter keyword: PRM, multiplexing, quantification, targeted proteomics, LC-MS/MS

Andreas Nitsche
contact affiliation	Robert Koch Institute Centre for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS1)
contact email	nitschea@rki.de
lab head
Joerg Doellinger
contact affiliation	Robert Koch Institute
contact email	Doellingerj@rki.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD017778
     1. Label: PRIDE project
     2. Name: Triggered offset fragmentation allows massively multiplexed target profiling on quadrupole-orbitrap mass spectrometers