PXD064019

PXD064019 is an original dataset announced via ProteomeXchange.

Title	Are Solid Particles Ready for Prime-Time Proteomics?
Description	In this work, we evaluate the performance of nonporous C-18 stationary phases in high-speed proteomics workflows. We employed two commercially available sub-2 µm nonporous particle (NPP) materials, ODSIIIE and SOLAD, to fabricate analytical columns using 150 µm internal diameter (i.d.) fused silica capillaries to ensure compatibility with nano-UHPLC and nano-HPLC pressure regimes. Using long NPP columns (15 – 25 cm) connected to a conventional nano-UHPLC, we found that both materials supported efficient peptide separations within the flow rate and pressure ranges typical of nano-UHPLC systems. Shorter columns (4 – 5 cm), used with the 10- and 16-minute Whisper Zoom 120 and Zoom 80 methods on the Evosep One HPLC, demonstrated competitive separation performance compared to columns packed with fully porous (FPP) and superficially porous particles (SPP), achieving full-width at half maximum (FWHM) values below 2 seconds (Zoom 120) and 3 seconds (Zoom 80). Peak shape remained consistent with sample loads up to 25 ng of a human cell lysate digest, a level well-suited to the sensitivity of modern mass spectrometers. DIA LC-MS/MS analysis of 20 ng from the same digest demonstrated that NPP columns provided comparable or superior performance relative to FPP and SPP materials, identifying approximately 23,000 precursors (~3,000 proteins) with Zoom 120 and ~33,000 precursors (~3,800 proteins) with Zoom 80. These findings establish NPP-based columns as a viable and competitive alternative to FPP and SPP materials, particularly suited for high-throughput and high-sensitivity proteomics applications.
HostingRepository	PRIDE
AnnounceDate	2025-08-27
AnnouncementXML	Submission_2025-08-27_07:42:43.569.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Eduardo Kitano
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-16 10:03:35	ID requested
⏵ 1	2025-08-27 07:42:43	announced

10.1021/ACS.ANALCHEM.5C03073;

submitter keyword: Bottom-up Proteomics, High-throughput LC-MS/MS, Reversed-phase chromatography, LC-MS/MS

Shabaz Mohammed
contact affiliation	Rosalind Franklin Institute, Harwell Campus, OX11 0QX Didcot, United Kingdom Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, United Kingdom Department of Chemistry, University of Oxford, OX1 3TA, Oxford, 16 United Kingdom
contact email	shabaz.mohammed@chem.ox.ac.uk
lab head
Eduardo Kitano
contact affiliation	Rosalind Franklin Institute, Harwell Campus, OX11 0QX Didcot, United Kingdom Department of Pharmacology, University of Oxford, OX1 3QT Oxford, United Kingdom
contact email	eduardo.kitano@rfi.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/2025/08/PXD064019

PRIDE project URI

• PRIDE
  1. PXD064019
     1. Label: PRIDE project
     2. Name: Are Solid Particles Ready for Prime-Time Proteomics?