PXD039808

PXD039808 is an original dataset announced via ProteomeXchange.

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

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.

10.6019/PXD039808;

submitter keyword: formalin-fixed, proteomics, brain, mass spectrometry, pathways, protein, region, method,human, signaling

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

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PRIDE project URI

• PRIDE
  1. PXD039808
     1. Label: PRIDE project
     2. Name: Inter-regional proteomic profiling of the human brain using optimized protein extraction method from formalin-fixed tissue to identify signaling pathways