MassIVE MSV000083970

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Top-down proteomics of medicinal cannabis.

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Description

The revised legislation on medicinal cannabis has triggered a surge of research study in this space. Yet cannabis proteomics is lagging. In a previous study, we have optimised the protein extraction of mature buds for bottom-up proteomics. In this follow-up study, we develop a top-down proteomics strategy to identify intact denatured protein from cannabis apical buds. After testing different SID, CID, HCD and ETD parameters on infused known protein standards, we devised three LC-MS/MS methods for top-down sequencing of cannabis proteins. Different MS/MS modes produce distinct spectra, albeit greatly overlapping between SID, CID and HCD. The number of fragments increased with the energy applied; however, this did not necessarily translate into greater sequence coverage. Some precursors are more amenable to fragmentation than other. Sequence coverage decreases as the mass of the protein increases. Combining all MS/MS data maximised AA sequence coverage, achieving 73 percents for myoglobin. In this experiment, most cannabis proteins were smaller than 30 kD. Out of the 11,250 MS/MS spectra generated, only 213 (2 percents) were annotated amounting to 20 protein identifications. Most identified proteins are involved in photosynthesis, translation, and ATP production. Only one protein belongs to the phytocannabinoid biosynthesis, olivetolic acid cyclase. doi:10.3390/proteomes7040033 [doi:10.25345/C56S7Z] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: infusion, LC-MS, LC-MS/MS, SID, CID, HCD, ETD, apical bud, cannabis intact proteins, protein standards, top-down sequencing

Contact

Principal Investigators:
(in alphabetical order) 		Delphine Vincent, Agriculture Victoria Research, Australia
Submitting User: delphine_1_2
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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.