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PXD027741

PXD027741 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLaser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain
DescriptionMass spectrometry (MS)-based spatially resolved top-down proteomics (TDP) of tissues is crucial for understanding the roles played by microenvironmental heterogeneity in the biological functions of organs and for discovering new proteoform biomarkers of diseases. There are few published spatially resolved TDP studies. One of the challenges relates to the limited performance of TDP for the analysis of spatially isolated samples using, for example, laser capture microdissection (LCM) because those samples are usually mass-limited. We present the first pilot study of LCM-capillary zone electrophoresis (CZE)-MS/MS for spatially resolved TDP and used zebrafish brain as the sample. The LCM-CZE-MS/MS platform employed a non-ionic detergent and a freeze-thaw method for efficient proteoform extraction from LCM isolated brain sections followed by CZE-MS/MS without any sample cleanup step, ensuring high sensitivity. Over 400 proteoforms were identified in a CZE-MS/MS analysis of one LCM brain section via consuming the protein content of roughly 250 cells. We observed drastic differences in proteoform profiles between two LCM brain sections isolated from the optic tectum (Teo) and telencephalon (Tel) regions. Proteoforms of three proteins (npy, penkb, and pyya) having neuropeptide hormone activity were exclusively identified in the isolated Tel section. Proteoforms of reticulon, myosin, and troponin were almost exclusively identified in the isolated Teo section, and those proteins play essential roles in visual and motor activities. The proteoform profiles accurately reflected the main biological functions of the Teo and Tel regions of the brain. Additionally, hundreds of post-translationally modified proteoforms were identified.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:39:06.619.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLiangliang Sun
SpeciesList scientific name: zebrafish metagenome; NCBI TaxID: 1331678;
ModificationListphosphorylated residue; acetylated residue; monohydroxylated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-08-05 08:59:59ID requested
12023-03-11 00:04:47announced
22023-11-14 08:39:07announced2023-11-14: Updated project metadata.
Publication List
Lubeckyj RA, Sun L, Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain. Mol Omics, 18(2):112-122(2022) [pubmed]
Keyword List
submitter keyword: spatially resolved top-down proteomics
capillary zone electrophoresis-tandem mass spectrometry
laser capture microdissection
zebrafish brain
proteoform
high sensitivity
neuropeptide hormone activity
motor activity
Contact List
Liangliang Sun
contact affiliationMichigan State University
contact emaillsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliationMichigan State University
contact emaillsun@chemistry.msu.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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