Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

Jenkins, Conor; Orsburn, Benjamin C.

doi:10.1101/567339

“…We have recently described the identification of approximately 1,000 distinct small molecule features present in extractions from mature cannabis flowers. 28 Six samples used in this previous study were also prepared for single shot LC-MS analysis using a variant of the IonStar methodology 29 as described above. These individual files were processed in PD 2.2 using SeQuest searched against the eggNOG FATA and utilizing the Minora algorithm for relative label free quantification according to manufacturer default settings.…”

Section: Correlation Analysis Of Small Molecules and Proteinsmentioning

confidence: 99%

The Cannabis Proteome Draft Map Project

Jenkins¹,

Orsburn²

2020

Preprint

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Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org

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“…Correlation analysis in proteomics has been shown to be a powerful tool in the identification of cooperating proteins in biological processes [32]. We have recently described the identification and quantification of over 1000 small molecule features in medicinal products [33]. While the pathways leading to the production of the major cannabinoids has been the focus of intense study, little is known regarding the production of other central and secondary metabolites.…”

Section: Correlation Analysis Between Small Molecules and Proteinsmentioning

confidence: 99%

“…We have recently described the identification of approximately 1000 distinct small molecule features present in extractions from mature cannabis flowers [33]. Six samples used in this previous study were also used for the proteomic study described herein.…”

Section: Correlation Analysis Of Small Molecules and Proteinsmentioning

confidence: 99%

The Cannabis Proteome Draft Map Project

Jenkins

¹

,

Orsburn

²

2020

IJMS

Self Cite

View full text Add to dashboard Cite

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.

show abstract

“…We have recently described the identification of approximately 1,000 distinct small molecule features present in extractions from mature cannabis flowers. 28 Six samples used in this previous study were also prepared for single shot LC-MS analysis using a variant of the IonStar methodology 29 as described above. These individual files were processed in PD 2.2 using SeQuest searched against the eggNOG FATA and utilizing the Minora algorithm for relative label free quantification according to manufacturer default settings.…”

Section: D Protein Library Construction and Similarity Scoringmentioning

confidence: 99%

The Cannabis Multi-Omics Draft Map Project

Jenkins

¹

,

Orsburn

²

2019

Preprint

Self Cite

View full text Add to dashboard Cite

Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which "next generation" DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that posttranslational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org Proteomics is a science dedicated to the creation of comprehensive quantitative snapshots of all the proteins produced by an individual organism, tissue or cell. 1 The term was coined in the 1990s during the efforts to sequence the first complete human genomes. 2 While the technology was in place to complete the human genome draft in 2003, the first two drafts of the human proteome were not completed by teams led by Johns Hopkins and CIPSM researchers until 2014. These two separate and ambitious projects were the composite of thousands of hours of instrument run time utilizing the most sophisticated hardware available at that time. 3,4 Recent advances in mass spectrometry technology now permit the completion of proteome profiles in more practical time. Single celled organisms have been "fully" sequenced in less than an hour, and by use of multi-dimensional chromatography, relatively high coverage human proteomes have been completed in only a few days. 5-7 While much can be learned by sequencing DNA and RNA in a cell, quantifying and sequencing the proteome has distinct advantages as proteins perform physical and enzymatic activities in the cell and ar...

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Application of Global Metabolomics to the Identification of Complex Counterfeit Medicinal Products

Cited by 3 publications

References 19 publications

The Cannabis Proteome Draft Map Project

The Cannabis Proteome Draft Map Project

The Cannabis Proteome Draft Map Project

The Cannabis Multi-Omics Draft Map Project

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