PXD039808 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Inter-regional proteomic profiling of the human brain using optimized protein extraction method from formalin-fixed tissue to identify signaling pathways |
Description | Proteomics offers vast potential to study the molecular regulation of the human brain. Formalin fixation is a common method for preserving human tissue, however, presents challenges for proteomic analysis. In this study we compared the efficiency of two different protein extraction buffers on three post-mortem, formalin-fixed human brains. Equal amounts of extracted proteins were subjected to in-gel tryptic digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein, peptide sequence and peptide group identifications, protein abundance and gene ontology pathways were analyzed. Protein extraction was superior using lysis buffer containing Tris (hydroxymethyl) aminomethane hydrochloride, sodium dodecyl sulfate, sodium deoxycholate, and Triton X-100 (TrisHCl, SDS, SDC, Triton X-100), which was then used for inter-regional analysis. Pre-frontal, motor, temporal, and occipital cortex tissue was analyzed by label free quantification (LFQ) proteomics, Ingenuity Pathway Analysis and PANTHERdb. Inter-regional analysis of the human brain revealed differential enrichment of proteins. We found similarly activated cellular signaling pathways, suggesting commonalities in the molecular regulation of neuroanatomically-linked brain functions. Overall, we developed an optimized, robust, and efficient method for protein extraction from formalin-fixed, human brain tissue for in-depth LFQ proteomics. We further demonstrate that this method is suitable for quick analysis of molecular signaling pathways in the human brain. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_09:00:35.922.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD039808 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Albert Lee |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-02-02 08:32:53 | ID requested | |
1 | 2023-02-22 07:33:10 | announced | |
⏵ 2 | 2023-11-14 09:00:36 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: formalin-fixed, proteomics, brain, mass spectrometry, pathways, protein, region, method,human, signaling |
Contact List
Albert Lee |
contact affiliation | Macquarie Medical School, Faculty of Medicine Health and Human Sciences, Macquarie University NSW 2109 Australia |
contact email | albert.lee@mq.edu.au |
lab head | |
Albert Lee |
contact affiliation | Macquarie University |
contact email | albert.lee@mq.edu.au |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039808
- Label: PRIDE project
- Name: Inter-regional proteomic profiling of the human brain using optimized protein extraction method from formalin-fixed tissue to identify signaling pathways