PXD069730-1

PXD069730 is an original dataset announced via ProteomeXchange.

Title	A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High Performance Proteomics Analysis: Bulk HeLa Data Sets for PAMAF, pDIA-PAMAF, and DDA Modes
Description	Here we present a novel data independent acquisition mass spectrometry operating mode termed parallel accumulation-mobility aligned fragmentation (PAMAF) that offers enhanced speed and sensitivity for ion fragmentation analysis for nontargeted discovery workflows such as bottom-up proteomics. This mode of operation leverages high-resolution ion mobility (HRIM) separation capabilities of the structures for lossless ion manipulation (SLIM) technology to achieve HRIM-based precursor isolation in place of traditional quadrupole filtering approaches. This PAMAF mode of operation increases the number of features that can be identified per MS1/MS2 acquisition cycle, by employing mobility-based time alignment to associate fragment ions with their corresponding precursor ions. By using a high-speed, lossless separation technique for precursor isolation instead of the comparatively slow and wasteful quadrupole filtering method, we can avoid ion losses up to 99% while simultaneously increasing the rate at which precursor ions are sequentially fragmented and detected. Additionally, by storing ions in a trapping region while the previous packet of ions is being analyzed, the PAMAF mode achieves close to ~100% ion utilization efficiency. Benchmarking results of LC-PAMAF-MS analysis of a standard whole cell protein digest showed approximately 6x more protein group identifications compared to a standard data-dependent acquisition (DDA) analysis without HRIM on the same QTOF instrument. Quantitative evaluations demonstrated that PAMAF mode was capable of quantifying low abundance peptides, including those undetectable by DDA. Additionally, since precursor isolation in PAMAF mode is size-based rather than m/z-based, many coeluting isobars and isomers can be resolved prior to fragmentation to eliminate chimeric spectra that compromise identification accuracy. In this work we also explored the benefits of combining HRIM and quadrupole isolation to achieve maximum specificity. This approach, known as DIA-PAMAF mode, further reduces the frequency of chimeric fragmentation spectra, and enabled the detection of over 8,000 protein groups from a HeLa digest analysis. PAMAF mode brings a powerful new technique to the field of proteomics that has the potential to improve the sensitivity and selectivity of mass spectrometry-based proteomics.
HostingRepository	PRIDE
AnnounceDate	2026-07-12
AnnouncementXML	Submission_2026-07-12_15:59:55.910.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leonard Rorrer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Mobilion MBI format; Agilent instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-21 09:46:46	ID requested
⏵ 1	2026-07-12 15:59:56	announced

Rorrer LC, Deng L, Royer L, Uribe I, Orsburn BC, Bernhardt O, Gandhi T, Reiter L, DeBord D, A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High-Performance Proteomics Analysis. Mol Cell Proteomics, 25(7):101608(2026) [pubmed]

10.1016/j.mcpro.2026.101608;

submitter keyword: Human, PAMAF, Ion Mobility, QTOF, SLIM, HeLa, HRIM, Bottom-Up Proteomics

Daniel DeBord
contact affiliation	MOBILion Systems, Inc.
contact email	daniel.debord@mobilionsystems.com
lab head
Leonard Rorrer
contact affiliation	MOBILion Systems, Inc.
contact email	leonard.rorrer@mobilionsystems.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/2026/07/PXD069730

PRIDE project URI

• PRIDE
  1. PXD069730
     1. Label: PRIDE project
     2. Name: A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High Performance Proteomics Analysis: Bulk HeLa Data Sets for PAMAF, pDIA-PAMAF, and DDA Modes