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Jakubec PJ, Doucette AA. Automated Electrokinetic Platform for High-Throughput Sodium Dodecyl Sulfate Depletion Ahead of Proteome Analysis by Mass Spectrometry. Anal Chem 2021; 93:14042-14047. [PMID: 34644045 DOI: 10.1021/acs.analchem.1c03549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sodium dodecyl sulfate (SDS) provides numerous benefits for proteome sample preparation. However, the surfactant can be detrimental to downstream mass spectrometry analysis. Although strategies are available to deplete SDS from proteins, each is plagued by unique deficiencies that challenge their utility for high-throughput proteomics. An optimal approach would rapidly and reproducibly achieve less than 10 ppm residual SDS while simultaneously maximizing analyte recovery. Here, we describe improvements to a simple electrokinetic device termed transmembrane electrophoresis, which we previously reported for automated, rapid SDS depletion of proteome samples. Voltage-driven transport of SDS across a molecular weight cutoff membrane is enhanced at higher electric fields, which is herein achieved by integrating an active cooling mechanism to mitigate the impacts of Joule heating. We report 99.9% reduction of SDS (final concentration < 5 ppm) in 5 min. The device is employed in a detergent-based proteomic workflow for analysis of an enriched yeast membrane proteome extract, demonstrating quantitative protein recovery (>98%) and increasing the number of identifications by liquid chromatography-tandem mass spectrometry.
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Affiliation(s)
- Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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2
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Ying Y, Li H. Recent progress in the analysis of protein deamidation using mass spectrometry. Methods 2020; 200:42-57. [PMID: 32544593 DOI: 10.1016/j.ymeth.2020.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Deamidation is a nonenzymatic and spontaneous posttranslational modification (PTM) that introduces changes in both structure and charge of proteins, strongly associated with aging proteome instability and degenerative diseases. Deamidation is also a common PTM occurring in biopharmaceutical proteins, representing a major cause of degradation. Therefore, characterization of deamidation alongside its inter-related modifications, isomerization and racemization, is critically important to understand their roles in protein stability and diseases. Mass spectrometry (MS) has become an indispensable tool in site-specific identification of PTMs for proteomics and structural studies. In this review, we focus on the recent advances of MS analysis in protein deamidation. In particular, we provide an update on sample preparation, chromatographic separation, and MS technologies at multi-level scales, for accurate and reliable characterization of protein deamidation in both simple and complex biological samples, yielding important new insight on how deamidation together with isomerization and racemization occurs. These technological progresses will lead to a better understanding of how deamidation contributes to the pathology of aging and other degenerative diseases and the development of biopharmaceutical drugs.
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Affiliation(s)
- Yujia Ying
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Huilin Li
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.
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3
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Li Y, Fang F, Sun M, Zhao Q, Hu Y, Sui Z, Liang Z, Zhang L, Zhang Y. Ionic liquid-assisted protein extraction method for plant phosphoproteome analysis. Talanta 2020; 213:120848. [PMID: 32200934 DOI: 10.1016/j.talanta.2020.120848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTM) and plays critical roles in maintaining many biological processes of plant species, such as being a significant signal related to resistance to tobacco mosaic virus (TMV) infection in tobacco. Compared to other organisms, in-depth profiling of plant phosphoproteome remains challenging due to the harsh extraction environment of plant proteins and low abundance of plant phosphorylation, generally requiring large amount of plant materials. Herein, we developed an integrated strategy for efficient sample preparation of amounts of plant tissues, by integrating ionic liquid (IL)-assisted protein extraction, in-solution digestion, precipitation-assisted IL removal, as well as immobilized metal ion affinity chromatography (IMAC) enrichment of phosphopeptides together. In this strategy, to improve the efficiency of protein extraction and enzymatic digestion, IL of 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was used as the solubilizer due to its excellent solubilizing ability and enzyme compatibility demonstrated in our previous work. Briefly, the extraction capability of C12Im-Cl for protein amount from tobacco leaves was improved 1.9-fold compared to the commonly used urea-assisted method. Notably, to avoid its interference with subsequent LC-MS analysis, the IL was easily removed from the peptide solution by our proposed ion substitution-mediated C12Im + precipitation strategy with high efficiency. By handling 10 mg of starting protein materials of tobacco leaves, 14,441 unique phosphopeptides, assigned to 5153 unique phosphoproteins were confidently identified. To the best of our knowledge, this was the most comprehensive phosphorylation dataset for tobacco so far. All the results demonstrated our strategy was of great potential to promote the large-scale analysis of plant phosphoproteome.
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Affiliation(s)
- Yang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fei Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mingwei Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510005, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yechen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
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Serra A, Gallart-Palau X, Koh WY, Chua ZJY, Guo X, Chow CJJ, Chen WM, Park JE, Li T, Tam JP, Sze SK. Prooxidant modifications in the cryptome of beef jerky, the deleterious post-digestion composition of processed meat snacks. Food Res Int 2019; 125:108569. [PMID: 31554040 DOI: 10.1016/j.foodres.2019.108569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/01/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023]
Abstract
Snacking has traditionally been associated with consumption of foods rich in fats and carbohydrates. However, new dietary trends switched to consumption of protein-rich foods. This study investigates the impact of food processing on the cryptome of one of the most widely consumed meat snacks, beef jerky. We have performed discovery-driven proteome-wide analyses, which identified a significantly elevated presence of reactive prooxidant post-translational modifications in jerky. We also found that these protein decorations impact an important subset of in-silico predicted DNA binding cryptides. Furthermore, we observed cell-dependent reduction in cell viability after prolonged treatments with endogenous-like jerky digests. Collectively these findings uncover the presence of prooxidant modifications in processed dried beef snacks and associate their presence with cytotoxicity. Thus, the findings reported here can pave the way for future studies aimed to establish appropriate dietary recommendations on snacking trends.
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Affiliation(s)
- Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; IMDEA-Food Research Institute, Campus of International Excellence UAM+CSIC, 8 Crta. Canto Blanco, Madrid, 28049, Spain
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; IMDEA-Food Research Institute, Campus of International Excellence UAM+CSIC, 8 Crta. Canto Blanco, Madrid, 28049, Spain
| | - Wei Yi Koh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Zoey Jia Yu Chua
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Xue Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Chase Jia Jing Chow
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Wei Meng Chen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Tianhu Li
- School of Physical & Mathematical Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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Yan J, Ding J, Jin G, Duan Z, Yang F, Li D, Zhou H, Li M, Guo Z, Chai W, Liang X. Profiling of Human Milk Oligosaccharides for Lewis Epitopes and Secretor Status by Electrostatic Repulsion Hydrophilic Interaction Chromatography Coupled with Negative-Ion Electrospray Tandem Mass Spectrometry. Anal Chem 2019; 91:8199-8206. [PMID: 31070893 DOI: 10.1021/acs.analchem.9b00687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human milk oligosaccharides (HMOs) are one of the most abundant ingredients in breast milk, and they play a beneficial role for newborns and are important for infant health. The peripheral fucosylated sequences of HMOs, such as the histo-blood group ABH(O) and Lewis a, b, x, and y antigens, are determined by the expression of the secretor (Se) and Lewis (Le) genes in the mammary gland, and are often the recognition motifs and serve as decoy receptors for microbes. In this work, we developed a method for determination of secretor status and Lewis blood phenotype and assignment of Lewis blood-group epitopes. The method was based on electrostatic repulsion/hydrophilic interaction chromatography coupled with tandem mass spectrometry (ERLIC-MS/MS). A specifically designed stationary phase, aspartic acid-bonded silica (ABS), was used to separate the acidic and neutral HMOs by electrostatic repulsion followed by HILIC. Negative-ion electrospray MS/MS was then used for analysis of secretor status and Lewis blood phenotypes and assignment of important epitopes of HMOs from the lactating mothers by selecting a specific set of unique fragment ions.
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Affiliation(s)
- Jingyu Yan
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
| | - Junjie Ding
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Gaowa Jin
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
| | - Zhaojun Duan
- National Institute for Viral Disease Control and Prevention , Beijing 102206 , China
| | - Fan Yang
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
| | - Dandi Li
- National Institute for Viral Disease Control and Prevention , Beijing 102206 , China
| | - Han Zhou
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
| | - Ming Li
- College of Basic Medical Science , Dalian Medical University , Dalian , China
| | - Zhimou Guo
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
| | - Wengang Chai
- Glycosciences Laboratory , Faculty of Medicine, Imperial College London , Hammersmith Campus, Du Cane Road , London W12 0NN , United Kingdom
| | - Xinmiao Liang
- Dalian Institute of Chemical Physics , Chinese Academy of Sciences, Key Laboratory of Separation Science for Analytical Chemistry , Dalian 116023 , China
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Waas M, Pereckas M, Lipinski RAJ, Ashwood C, Gundry RL. SP2: Rapid and Automatable Contaminant Removal from Peptide Samples for Proteomic Analyses. J Proteome Res 2019; 18:1644-1656. [PMID: 30795648 PMCID: PMC6571012 DOI: 10.1021/acs.jproteome.8b00916] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptide cleanup is essential for the removal of contaminating substances that may be introduced during sample preparation steps in bottom-up proteomic workflows. Recent studies have described benefits of carboxylate-modified paramagnetic particles over traditional reversed-phase methods for detergent and polymer removal, but challenges with reproducibility have limited the widespread implementation of this approach among laboratories. To overcome these challenges, the current study systematically evaluated key experimental parameters regarding the use of carboxylate-modified paramagnetic particles and determined those that are critical for maximum performance and peptide recovery and those for which the protocol is tolerant to deviation. These results supported the development of a detailed, easy-to-use standard operating protocol, termed SP2, which can be applied to remove detergents and polymers from peptide samples while concentrating the sample in solvent that is directly compatible with typical LC-MS workflows. We demonstrate that SP2 can be applied to phosphopeptides and glycopeptides and that the approach is compatible with robotic liquid handling for automated sample processing. Altogether, the results of this study and accompanying detailed operating protocols for both manual and automated processing are expected to facilitate reproducible implementation of SP2 for various proteomics applications and will especially benefit core or shared resource facilities where unknown or unexpected contaminants may be particularly problematic.
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Affiliation(s)
- Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael Pereckas
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Christopher Ashwood
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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7
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Gallart-Palau X, Serra A, Hase Y, Tan CF, Chen CP, Kalaria RN, Sze SK. Brain-derived and circulating vesicle profiles indicate neurovascular unit dysfunction in early Alzheimer's disease. Brain Pathol 2019; 29:593-605. [PMID: 30629763 DOI: 10.1111/bpa.12699] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/20/2018] [Indexed: 12/28/2022] Open
Abstract
Vascular factors that reduce blood flow to the brain are involved in apparition and progression of dementia. We hypothesized that cerebral hypoperfusion (CH) might alter the molecular compositions of brain intercellular communication mechanisms while affecting the neurovascular unit in preclinical and clinical human dementias. To test that hypothesis, mice were subjected to bilateral common carotid stenosis (BCAS) and the molecular compositions of brain-derived and circulating extracellular vesicles (EVs) were assessed. Murine brain vesicle profiles were then analyzed in parallel with brain EVs from post-mortem subjects affected by preclinical Alzheimer's Disease (AD) and mixed dementias. Brain EVs were identified with molecular mediators of hypoxia responses, neuroprotection and neurotoxicity in BCAS mice, patterns also partially resembled by subjects with preclinical AD and mixed dementias. Together these findings indicate that brain EVs represent a promising source of therapeutic targets and circulating markers of neurovascular insult in idiopathic dementias. Furthermore, the results obtained generate novel and compelling hypotheses about the molecular involvement of the vascular component in the etiology of human dementias.
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Affiliation(s)
- Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoshiki Hase
- Institute of Neuroscience, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, UK
| | - Chee Fan Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Christopher P Chen
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Raj N Kalaria
- Institute of Neuroscience, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, UK
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Ghiasvand A, Feng Z, Quirino JP. Enrichment and Separation of Cationic, Neutral, and Chiral Analytes by Micelle to Cyclodextrin Stacking–Micellar Electrokinetic Chromatography. Anal Chem 2018; 91:1752-1757. [DOI: 10.1021/acs.analchem.8b03542] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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