PXD056492

PXD056492 is an original dataset announced via ProteomeXchange.

Title	Impact of local air pressure on ion mobilities and data consistency in diaPASEF-based high throughput proteomics
Description	Data-independent acquisition (DIA) on ion mobility – TOF hybrid mass spectrometers enables deep proteome coverage and high data completeness in large-scale proteomics studies. For advanced acquisition schemes such as parallel accumulation serial fragmentation-based DIA (diaPASEF) stability of ion mobility (1/K0) over time is crucial for consistent data quality. We found that minor changes in environmental air pressure systematically affect vacuum pressure in the TIMS analyzer, causing ion mobility shifts. By comparing experimental ion mobilities with historical weather data, we attributed observed drifts to daily fluctuations in ground air pressure. These drifts negatively impact peptide quantification across consecutively acquired samples due to drift-dependent abundance changes and increased missing values for ions located at the boundaries of diaPASEF isolation windows, which cannot be corrected by post-processing. To address this, we applied an in-batch mobility autocalibration feature on a run-wise basis, leading to full elimination of ion mobility drifts.
HostingRepository	PRIDE
AnnounceDate	2025-01-25
AnnouncementXML	Submission_2025-01-24_21:06:22.112.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sascha Knecht
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methionine oxidation with neutral loss of 80 Da; acetylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-03 19:25:20	ID requested
⏵ 1	2025-01-24 21:06:22	announced

10.1021/ACS.JPROTEOME.4C00932;

submitter keyword: TIMS, DIA,Proteomics, diaPASEF, high-throughput, data-independent acquisition, ion mobility

Nico Zinn
contact affiliation	Target Discovery, GSK/Cellzome
contact email	nico.x.zinn@gsk.com
lab head
Sascha Knecht
contact affiliation	Target Discovery, GSK / Cellzome
contact email	sascha.knecht@me.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/2025/01/PXD056492

PRIDE project URI

• PRIDE
  1. PXD056492
     1. Label: PRIDE project
     2. Name: Impact of local air pressure on ion mobilities and data consistency in diaPASEF-based high throughput proteomics