PXD029729 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | In-depth mass spectrometry-based proteomics of formalin-fixed, paraffin embedded tissues with a spatial resolution of 50–200 µm |
Description | Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories as a cost-effective means of preserving invaluable specimens for subsequent study, including for clinical proteomics in translational medicine. With the rapid growth of spatial proteomics, FFPE tissue samples can serve as a more accessible alternative to commonly used fresh frozen tissues. However, extracting proteins from FFPE tissue for analysis by mass spectrometry has been challenging due to crosslinks formed between proteins and formalin, particularly when studying limited samples. We have previously demonstrated that nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) is an enabling technology for high-resolution and in-depth spatial and single-cell proteomics measurements, but only fresh frozen tissues had been previously analyzed. Here we have adapted the nanoPOTS sample processing workflows for proteome profiling of 10-µm-thick FFPE tissues with lateral dimensions as small as 50 µm. Following a comparison of extraction solvents, times, and temperatures, and under the most favorable conditions, we respectively identified an average of 1180 and 2990 proteins from FFPE preserved mouse liver tissues having dimensions of 50 µm and 200 µm. This was on average 87% of the coverage achieved for fresh frozen mouse liver samples analyzed with the same general procedure. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. These workflows provide the greatest depth of coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:53:51.751.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Ryan Kelly |
SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-11-12 08:01:10 | ID requested | |
1 | 2022-08-01 20:01:13 | announced | |
⏵ 2 | 2023-11-14 08:53:52 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Fresh Frozen, Spatial, DDM,FFPE, LCM |
Contact List
Ryan T Kelly |
contact affiliation | Department of Chemistry and Biochemistry, Brigham Young University. |
contact email | ryan@chem.byu.edu |
lab head | |
Ryan Kelly |
contact affiliation | Brigham Young University |
contact email | ryan.kelly@byu.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD029729
- Label: PRIDE project
- Name: In-depth mass spectrometry-based proteomics of formalin-fixed, paraffin embedded tissues with a spatial resolution of 50–200 µm