PXD029902-1

PXD029902 is an original dataset announced via ProteomeXchange.

Title	A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline
Description	Here, we present a standardized, “off-the-shelf” proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlining a fully automated sample preparation platform, data independent acquisition (DIA) coupled with high field asymmetric waveform ion mobility spectrometer (FAIMS) interface, and an optimized library-free DIA database search strategy. Our systematic evaluation of FAIMS-DIA showed single compensation voltage (CV) at -35V not only yields deepest proteome coverage but also best correlates with DIA without FAIMS. Our in-depth comparison of direct-DIA database search engines showed Spectronaut outperforms others, providing highest quantifiable proteins. Next, we apply three common DIA strategies in characterizing human induced pluripotent stem cell (iPSC)-derived neurons and show single-shot MS using single CV(-35V)-FAIMS-DIA results in >9,000 quantifiable proteins with < 10% missing values, as well as superior reproducibility and accuracy compared to other existing DIA methods.
HostingRepository	PRIDE
AnnounceDate	2023-08-23
AnnouncementXML	Submission_2023-08-22_16:51:21.118.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yue AndyQi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-24 06:35:15	ID requested
⏵ 1	2023-08-22 16:51:21	announced

Dataset with its publication pending

submitter keyword: DIA, iPSC, temporal proteomics, Neurodegenerative, Single-shot,FAIMS

Yue AndyQi
contact affiliation	Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, USA
contact email	Andy.qi@nih.gov
lab head
Yue AndyQi
contact affiliation	National Cancer Institute/NIH
contact email	andy.qi@nih.gov
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/2023/08/PXD029902

PRIDE project URI

• PRIDE
  1. PXD029902
     1. Label: PRIDE project
     2. Name: A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline