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Sakarin S, Rungsipipat A, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Surachetpong S. Phosphoproteomics analysis of serum from dogs affected with pulmonary hypertension secondary to degenerative mitral valve disease. PeerJ 2024; 12:e17186. [PMID: 38708342 PMCID: PMC11067895 DOI: 10.7717/peerj.17186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/11/2024] [Indexed: 05/07/2024] Open
Abstract
Pulmonary hypertension (PH), a common complication in dogs affected by degenerative mitral valve disease (DMVD), is a progressive disorder characterized by increased pulmonary arterial pressure (PAP) and pulmonary vascular remodeling. Phosphorylation of proteins, impacting vascular function and cell proliferation, might play a role in the development and progression of PH. Unlike gene or protein studies, phosphoproteomic focuses on active proteins that function as end-target proteins within signaling cascades. Studying phosphorylated proteins can reveal active contributors to PH development. Early diagnosis of PH is crucial for effective management and improved clinical outcomes. This study aimed to identify potential serum biomarkers for diagnosing PH in dogs affected with DMVD using a phosphoproteomic approach. Serum samples were collected from healthy control dogs (n = 28), dogs with DMVD (n = 24), and dogs with DMVD and PH (n = 29). Phosphoproteins were enriched from the serum samples and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Data analysis was performed to identify uniquely expressed phosphoproteins in each group and differentially expressed phosphoproteins among groups. Phosphoproteomic analysis revealed nine uniquely expressed phosphoproteins in the serum of dogs in the DMVD+PH group and 15 differentially upregulated phosphoproteins in the DMVD+PH group compared to the DMVD group. The phosphoproteins previously implicated in PH and associated with pulmonary arterial remodeling, including small nuclear ribonucleoprotein G (SNRPG), alpha-2-macroglobulin (A2M), zinc finger and BTB domain containing 42 (ZBTB42), hemopexin (HPX), serotransferrin (TRF) and complement C3 (C3), were focused on. Their unique expression and differential upregulation in the serum of DMVD dogs with PH suggest their potential as biomarkers for PH diagnosis. In conclusion, this phosphoproteomic study identified uniquely expressed and differentially upregulated phosphoproteins in the serum of DMVD dogs with PH. Further studies are warranted to validate the diagnostic utility of these phosphoproteins.
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Affiliation(s)
- Siriwan Sakarin
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
| | - Anudep Rungsipipat
- Center of Excellence for Companion Animal Cancer, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand, Bangkok, Thailand
| | - Sirilak Surachetpong
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, Bangkok, Thailand
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Sakarin S, Rungsipipat A, Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Surachetpong SD. Proteomic analysis of the serum in dogs with pulmonary hypertension secondary to myxomatous mitral valve disease: the preliminary study. Front Vet Sci 2024; 11:1327453. [PMID: 38596466 PMCID: PMC11002142 DOI: 10.3389/fvets.2024.1327453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Background Pulmonary hypertension (PH) is a common complication in dogs with myxomatous mitral valve disease (MMVD), characterized by elevated blood pressure in pulmonary artery. Echocardiography is a reliable technique for PH diagnosis in veterinary medicine. However, it is limited to use as an early detection method. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has found extensive application in the discovery of serum protein biomarkers for various diseases. The objective of this study was to identify serum proteins in healthy control dogs and MMVD dogs both with and without PH using LC-MS/MS. Materials and methods In this research, a total of 81 small-breed dogs participated, and they were categorized into three groups: the control (n = 28), MMVD (n = 24) and MMVD+PH (n = 29) groups. Serum samples were collected and analyzed by LC-MS/MS. Results Differentially expressed proteins were identified, and the upregulated and downregulated proteins in MMVD+PH group including Myomesin 1 (MYOM1) and Histone deacetylase 7 (HDAC7), Pleckstrin homology domain containing M3 (PLEKHM3), Diacylglycerol lipase alpha (DAGLA) and Tubulin tyrosine ligase like 6 (TTLL6) were selected as proteins of interest in MMVD dogs with PH. Conclusion Different types of proteins have been identified in healthy dogs and MMVD dogs with and without PH. Additional studies are needed to investigate the potential of these proteins as biomarkers for PH in dogs with MMVD.
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Affiliation(s)
- Siriwan Sakarin
- Faculty of Veterinary Science, Department of Veterinary Medicine, Center of Excellence for Companion Animal Cancer, Chulalongkorn University, Bangkok, Thailand
| | - Anudep Rungsipipat
- Faculty of Veterinary Science, Department of Pathology, Chulalongkorn University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sirilak Disatian Surachetpong
- Faculty of Veterinary Science, Department of Veterinary Medicine, Center of Excellence for Companion Animal Cancer, Chulalongkorn University, Bangkok, Thailand
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Puliasis SS, Lewandowska D, Hemsley PA, Zhang R. ProtView: A Versatile Tool for In Silico Protease Evaluation and Selection in a Proteomic and Proteogenomic Context. J Proteome Res 2023. [PMID: 37248202 DOI: 10.1021/acs.jproteome.3c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many tools have been created to generate in silico proteome digests with different protease enzymes and provide useful information for selecting optimal digest schemes for specific needs. This can save on time and resources and generate insights on the observable proteome. However, there remains a need for a tool that evaluates digest schemes beyond protein and amino acid coverages in the proteomic domain. Here, we present ProtView, a versatile in silico protease combination digest evaluation workflow that maps in silico-digested peptides to both protein and genome references, so that the potential observable portions of the proteome, transcriptome, and genome can be identified. The proteomic identification and quantification of evidence for transcriptional, co-transcriptional, post-transcriptional, translational, and post-translational regulation can all be examined in silico with ProtView prior to an experiment. Benchmarking against biological data comparing multiple proteases shows that ProtView can correctly estimate performances among the digest schemes. ProtView provides this information in a way that is easy to interpret, allowing for digest schemes to be evaluated before carrying out an experiment, in context that can optimize both proteomic and proteogenomic experiments. ProtView is available at https://github.com/SSPuliasis/ProtView.
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Affiliation(s)
- Sophia S Puliasis
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Piers A Hemsley
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK
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Gao Y, Sun Z, Guo Y, Qiang Z, Ben W. Virus inactivation by sequential ultraviolet-chlorine disinfection: Synergistic effect and mechanism. CHEMOSPHERE 2023; 314:137632. [PMID: 36565762 PMCID: PMC9770000 DOI: 10.1016/j.chemosphere.2022.137632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The COVID-19 outbreak has raised concerns about the efficacy of the disinfection process followed in water treatment plants in preventing the spread of viruses. Ultraviolet (UV) and chlorine multi-barrier disinfection processes are commonly used in water treatment plants; however, their effects on virus inactivation are still unclear. In this study, the effects of different disinfection processes (i.e., UV, free chlorine, and their combination) on waterborne viruses were analyzed using bacteriophage surrogates (i.e., MS2 and PR772) as alternative indicators. The results showed that the inactivation rates of PR772 by either UV or free chlorine disinfection were higher than those of MS2. PR772 was approximately 1.5 times more sensitive to UV disinfection and 8.4 times more sensitive to chlorine disinfection than MS2. Sequential UV-chlorine disinfection had a synergistic effect on virus inactivation, which was enhanced by an increase in the UV dose. As compared with single free chlorine disinfection, UV irradiation at 40 mJ cm-2 enhanced MS2 and PR772 inactivation significantly with a 2.7-fold (MS2) and a 1.7-fold (PR772) increase in the inactivation rate constants on subsequent chlorination in phosphate buffered saline. The synergistic effect was also observed in real wastewater samples, in which the MS2 inactivation rate increased 1.4-fold on subsequent chlorination following UV irradiation at 40 mJ cm-2. The mechanism of the synergistic effect of sequential UV-chlorine disinfection was determined via sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using MS2 as an indicator. The results showed that the synergistic effect was due to damage to MS2 surface proteins caused by previous UV disinfection, which enhanced the sensitivity of MS2 to chlorination. This study provides a feasible approach for the efficient inactivation of viruses in water supply and drainage.
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Affiliation(s)
- Ying Gao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Sun
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Ying Guo
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiwei Ben
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China.
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Vincent D, Bui A, Ram D, Ezernieks V, Bedon F, Panozzo J, Maharjan P, Rochfort S, Daetwyler H, Hayden M. Mining the Wheat Grain Proteome. Int J Mol Sci 2022; 23:ijms23020713. [PMID: 35054899 PMCID: PMC8775872 DOI: 10.3390/ijms23020713] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/23/2021] [Accepted: 12/30/2021] [Indexed: 12/10/2022] Open
Abstract
Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).
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Affiliation(s)
- Delphine Vincent
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
- Correspondence:
| | - AnhDuyen Bui
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
| | - Doris Ram
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
| | - Vilnis Ezernieks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC 3083, Australia;
| | - Joe Panozzo
- Agriculture Research Victoria, 110 Natimuk Road, Horsham, VIC 3400, Australia; (J.P.); (P.M.)
- Centre for Agricultural Innovation, University of Melbourne, Parkville, VIC 3010, Australia
| | - Pankaj Maharjan
- Agriculture Research Victoria, 110 Natimuk Road, Horsham, VIC 3400, Australia; (J.P.); (P.M.)
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia; (A.B.); (D.R.); (V.E.); (S.R.); (H.D.); (M.H.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
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Pradhan G, Sneha JM, Sonwane BP, Santhakumari B, Rao A, Kulkarni MJ. Multiple-parallel-protease digestion coupled with high-resolution mass spectrometry: An approach towards comprehensive peptide mapping of therapeutic mAbs. J Proteomics 2020; 232:104053. [PMID: 33238212 DOI: 10.1016/j.jprot.2020.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 11/18/2022]
Abstract
Therapeutic monoclonal antibodies (mAbs) are structurally large and complex molecules. To be safe and efficacious, a biosimilar mAb must show high similarity to its reference product in Critical Quality Attributes (CQA). mAbs are highly sensitive to protein expression, production, manufacturing, supply chain, and storage conditions. All these factors make biosimilar mAbs intrinsically susceptible for variability during production. Accordingly, several lots of references and tests are required to establish the biosimilarity of a test mAb. The primary structure is a CQA of a mAb affecting its safety and efficacy. Here, we apply peptide mapping as an analytical method to decipher the primary structure and associated modifications for a quick quality assessment of TrastuzumAb and RituximAb innovator and biosimilar. A multiple-parallel-protease digestion strategy followed by high-resolution mass spectrometric analysis consistently achieved 100% sequence coverage along with reliable detection of post-translational modifications. Additionally, the use of supporting methods such as intact mass analysis and circular dichroism helped us to decipher the primary and higher order structures of these mAbs. We identify discernible variations in the profile of the innovator and biosimilar mAbs and validate the method for quick yet deep comparability analysis of the primary structure of biosimilar mAbs sold in the market. SIGNIFICANCE: Peptide mapping using bottom-up approach is one of the most common methods for the characterization of therapeutic monoclonal antibodies. Herein, we describe a multi-parallel-protease digestion strategy using a combination of five different proteases followed by high-resolution mass spectrometric analysis with TrastuzumAb and RituximAb as an example. This resulted in a comprehensive identification of peptides with increased reliability and identification of different PTMs. Additional supporting orthogonal methods like intact mass and higher-order structure analysis helped evaluate broader conformational properties.
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Affiliation(s)
- Gauri Pradhan
- CSIR-National Chemical Laboratory, Pune 411008, India
| | - J M Sneha
- CSIR-National Chemical Laboratory, Pune 411008, India
| | - Babasaheb P Sonwane
- CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
| | - B Santhakumari
- CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research, Ghaziabad 201 002, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research, Ghaziabad 201 002, India.
| | - Mahesh J Kulkarni
- CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research, Ghaziabad 201 002, India.
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Comparison of Three Glycoproteomic Methods for the Analysis of the Secretome of CHO Cells Treated with 1,3,4- O-Bu 3ManNAc. Bioengineering (Basel) 2020; 7:bioengineering7040144. [PMID: 33182731 PMCID: PMC7712478 DOI: 10.3390/bioengineering7040144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/24/2020] [Accepted: 11/06/2020] [Indexed: 01/08/2023] Open
Abstract
Comprehensive analysis of the glycoproteome is critical due to the importance of glycosylation to many aspects of protein function. The tremendous complexity of this post-translational modification, however, makes it difficult to adequately characterize the glycoproteome using any single method. To overcome this pitfall, in this report we compared three glycoproteomic analysis methods; first the recently developed N-linked glycans and glycosite-containing peptides (NGAG) chemoenzymatic method, second, solid-phase extraction of N-linked glycoproteins (SPEG), and third, hydrophilic interaction liquid chromatography (HILIC) by characterizing N-linked glycosites in the secretome of Chinese hamster ovary (CHO) cells. Interestingly, the glycosites identified by SPEG and HILIC overlapped considerably whereas NGAG identified many glycosites not observed in the other two methods. Further, utilizing enhanced intact glycopeptide identification afforded by the NGAG workflow, we found that the sugar analog 1,3,4-O-Bu3ManNAc, a "high flux" metabolic precursor for sialic acid biosynthesis, increased sialylation of secreted proteins including recombinant human erythropoietin (rhEPO).
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The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines. Proteomes 2020; 8:proteomes8020013. [PMID: 32549361 PMCID: PMC7356525 DOI: 10.3390/proteomes8020013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
Cannabis research has taken off since the relaxation of legislation, yet proteomics is still lagging. In 2019, we published three proteomics methods aimed at optimizing protein extraction, protein digestion for bottom-up and middle-down proteomics, as well as the analysis of intact proteins for top-down proteomics. The database of Cannabis sativa proteins used in these studies was retrieved from UniProt, the reference repositories for proteins, which is incomplete and therefore underrepresents the genetic diversity of this non-model species. In this fourth study, we remedy this shortcoming by searching larger databases from various sources. We also compare two search engines, the oldest, SEQUEST, and the most popular, Mascot. This shotgun proteomics experiment also utilizes the power of parallel digestions with orthogonal proteases of increasing selectivity, namely chymotrypsin, trypsin/Lys-C and Asp-N. Our results show that the larger the database the greater the list of accessions identified but the longer the duration of the search. Using orthogonal proteases and different search algorithms increases the total number of proteins identified, most of them common despite differing proteases and algorithms, but many of them unique as well.
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