PXD065853

PXD065853 is an original dataset announced via ProteomeXchange.

Title	A novel ultra-high resolution multi-reflecting time-of-flight mass spectrometer in Y-MRT configuration for bottom-up proteomics
Description	The first results of using a new type of ultrahigh-resolution mass analyzer based on a planar multi-pass time-of-flight mass spectrometer with periodic reflecting lenses (Y-MRT MS) for bottom-up whole-proteome analysis are presented. The instrument achieves a resolving power of 1,000,000 for peptides across an m/z range of 200-2000, with a high repetition rate of 300 Hz (averaged to 1 Hz for enhanced dynamic range). In preliminary experiments, a single 30-minute gradient HPLC separation of 1 µg proteolytic cell digest yielded over 3700 protein groups (4500 at 5% FDR) in DirectMS1 mode (without fragmentation). Combining three technical runs increased this to 5200 protein groups at 5% FDR. Peptide ion mass measurements demonstrated an accuracy of 100-150 ppb across the whole m/z range, with a dynamic range exceeding 10⁴. In DIA mode (SWATH-DIA, 20 Th window, 30-minute gradient), 4200 protein IDs were obtained at 1% FDR. These results highlight Y-MRT mass analyzer potential as a powerful addition to existing high resolution mass spectrometers for bottom-up proteomics. Further improvements in proteome coverage and analysis time are anticipated with optimized HPLC configurations and the integration of gas-phase ion mobility separation.
HostingRepository	PRIDE
AnnounceDate	2025-11-05
AnnouncementXML	Submission_2025-11-05_04:33:55.781.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mark Ivanov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	time-of-flight

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-07 09:35:11	ID requested
⏵ 1	2025-11-05 04:33:56	announced

10.1021/ACS.ANALCHEM.5C04182;

submitter keyword: DIA, LC-MS1,TOF

Mikhail. V. Gorshkov
contact affiliation	V. L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
contact email	mike.gorshkov@gmail.com
lab head
Mark Ivanov
contact affiliation	INEP CP RAS
contact email	markmipt@gmail.com
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/2025/11/PXD065853

PRIDE project URI

• PRIDE
  1. PXD065853
     1. Label: PRIDE project
     2. Name: A novel ultra-high resolution multi-reflecting time-of-flight mass spectrometer in Y-MRT configuration for bottom-up proteomics