PXD068463-1

PXD068463 is an original dataset announced via ProteomeXchange.

Title	High Dynamic Range peptide mass spectrometry using segmented precursor ions accumulation - Plasma
Description	Limited sensitivity and depth of proteome sampling in experiments using Data-Dependent Acquisition (DDA) mass spectrometry are usually attributed to insufficient rate of fragmentation spectra acquisition relative to the number of co-eluting potential targets. Here we demonstrated that limited sensitivity and dynamic range of MS1 scans reduces the detection of low intensity ion, and thus their selection for fragmentation. As abundant ions occupy a large fraction of the ion accumulation capacity, we sought to improve MS1 detection of rare analytes by an easily implementable strategy based on gas-phase segmentation of the MS1 scan range, followed by co-accumulation and detection of all ions. The quadrupolar isolation windows used to segment the MS1 scan range are designed to transmit on average an equal number of charges, consistent with the parameter used by many recent mass spectrometers to regulate ion trap filling. This strategy, which we named High Dynamic Range MS1 (HDR-MS1), reduces the contribution of abundant ions to reaching the maximum ion capacity. As a result, HDR MS1 showed improved dynamic range and sensitivity compared to conventional full range scans, resulting in higher number of peptides and protein identifications under identical MS2 parameters, less redundant precursor ion sampling, and higher rate of quantified precursor ions. HDR MS1 scans are compatible with any DDA precursor selection filter and MS2 parameter, and the generated files can be analyzed using any software for peptide-spectral matching and quantification. This experiments refer to the plasma analysis
HostingRepository	MassIVE
AnnounceDate	2025-10-14
AnnouncementXML	Submission_2025-10-14_07:22:26.454.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paolo Cifani
SpeciesList	scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090;
ModificationList	Oxidation; Carboxymethyl
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-17 13:16:39	ID requested
⏵ 1	2025-10-14 07:22:27	announced

no publication

submitter keyword: gas-phase fractionation, DDA, Mouse plasma, DatasetType:Proteomics

Paolo Cifani
contact affiliation	Cold Spring Harbor Laboratory
contact email	cshl.mass.spec@gmail.com
lab head
Paolo Cifani
contact affiliation	Cold Spring Harbor Laboratory
contact email	cshl.mass.spec@gmail.com
dataset submitter

MassIVE dataset URI

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