PXD056436-1

PXD056436 is an original dataset announced via ProteomeXchange.

Title	Deep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type
Description	As the immune cells of the brain, microglia play a key role in various homeostatic and disease-related processes. In order to carry out their numerous functions, microglia are able to adopt a wide range of phenotypic states. The proteomic landscape represents a more accurate molecular representation of these phenotypes; however, microglia present unique challenges for proteomic analysis. This study implemented a streamlined liquid- and gas-phase fractionation method with data-dependent acquisition (DDA) and parallel accumulation serial fragmentation (PASEF) analysis on a TIMS-TOF instrument to compile a comprehensive protein library obtained from adult-derived, immortalized mouse microglia with minimal starting material (10µg). The empirical library consisted of 9,140 microglial proteins and was utilized to identify an average of 7,264 proteins per run from single-shot, DIA-based analysis of microglia. Additionally, a predicted library facilitated identification of 7,519 average proteins per run from the same DIA data, revealing complementary coverage compared to the empirical library and collectively increased coverage to approximately 8,000 proteins. Importantly, several immune response pathways were uniquely identified with empirical library approach. Overall, we report a simplified, reproducible approach for deep proteome coverage of microglia with low sample input and show the importance of library optimization for this phenotypically diverse cell type.
HostingRepository	PRIDE
AnnounceDate	2025-03-31
AnnouncementXML	Submission_2025-03-31_12:31:22.405.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stanley Stevens
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-01 19:07:18	ID requested
⏵ 1	2025-03-31 12:31:22	announced

10.3390/PROTEOMES12040035;

submitter keyword: DIA-PASEF, DDA library generation, deep proteomics,Microglia, DIA methods development

Dr. Stanley Stevens
contact affiliation	Dept. of MBS, University of South Florida
contact email	smstevens@usf.edu
lab head
Stanley Stevens
contact affiliation	University of South Florida
contact email	smstevens@usf.edu
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/2025/03/PXD056436

PRIDE project URI

• PRIDE
  1. PXD056436
     1. Label: PRIDE project
     2. Name: Deep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type