PXD041412

PXD041412 is an original dataset announced via ProteomeXchange.

Title	Filter-aided expansion proteomics
Description	Hydrogel-based tissue expansion combined with mass spectrometry (MS) offers an emerging spatial proteomics approach. Here, we present a filter-aided expansion proteomics (FAXP) strategy for spatial proteomics analysis of archived formalin-fixed paraffin-embedded (FFPE) specimens. Compared to our previous ProteomEx method, FAXP employed a customized tip device to enhance both the stability and throughput of sample preparation, thus guaranteeing the reproducibility and robustness of the workflow. FAXP achieved a 14.5-fold increase in volumetric resolution. It generated over 8 times higher peptide yield and a 255% rise in protein identifications while reducing sample preparation time by 50%. We also demonstrated the applicability of FAXP using human colorectal FFPE tissue samples. Furthermore, for the first time, we achieved bona fide single-subcellular proteomics under image guidance by integrating FAXP with laser capture microdissection.
HostingRepository	PRIDE
AnnounceDate	2024-10-02
AnnouncementXML	Submission_2024-10-01_19:25:38.558.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tiannan Guo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-08 01:29:20	ID requested
⏵ 1	2024-10-01 19:25:38	announced

Dataset with its publication pending

submitter keyword: mass spectrometry,Tissue expansion, FFPE, spatial proteomics, data-independent acquisition, colorectal cancer

Tiannan Guo
contact affiliation	Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
contact email	guotiannan@westlake.edu.cn
lab head
Tiannan Guo
contact affiliation	Westlake University
contact email	guotiannan@westlake.edu.cn
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/2024/10/PXD041412

PRIDE project URI

• PRIDE
  1. PXD041412
     1. Label: PRIDE project
     2. Name: Filter-aided expansion proteomics