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Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
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2
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Gong S, Hu X, Chen S, Sun B, Wu JL, Li N. Dual roles of drug or its metabolite-protein conjugate: Cutting-edge strategy of drug discovery using shotgun proteomics. Med Res Rev 2022; 42:1704-1734. [PMID: 35638460 DOI: 10.1002/med.21889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 11/11/2022]
Abstract
Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug-protein conjugates or metabolite-protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.
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Affiliation(s)
- Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Xiaolan Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Shengshuang Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Respiratory Medical Center, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
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IKK β mediates homeostatic function in inflammation via competitively phosphorylating AMPK and I κB α. Acta Pharm Sin B 2022; 12:651-664. [PMID: 35256937 PMCID: PMC8897026 DOI: 10.1016/j.apsb.2021.09.012] [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: 06/02/2021] [Revised: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 12/30/2022] Open
Abstract
Inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ) is one of important kinases in inflammation to phosphorylate inhibitor of nuclear factor kappa-B (IκBα) and then activate nuclear factor kappa-B (NF-κB). Inhibition of IKKβ has been a therapeutic strategy for inflammatory and autoimmune diseases. Here we report that IKKβ is constitutively activated in healthy donors and healthy IkkβC46A (cysteine 46 mutated to alanine) knock-in mice although they possess intensive IKKβ–IκBα–NF-κB signaling activation. These indicate that IKKβ activation probably plays homeostatic role instead of causing inflammation. Compared to IkkβWT littermates, lipopolysaccharides (LPS) could induce high mortality rate in IkkβC46A mice which is correlated to breaking the homeostasis by intensively activating p-IκBα–NF-κB signaling and inhibiting phosphorylation of 5ʹ adenosine monophosphate-activated protein kinase (p-AMPK) expression. We then demonstrated that IKKβ kinase domain (KD) phosphorylates AMPKα1 via interacting with residues Thr183, Ser184, and Thr388, while IKKβ helix–loop–helix motifs is essential to phosphorylate IκBα according to the previous reports. Kinase assay further demonstrated that IKKβ simultaneously catalyzes phosphorylation of AMPK and IκBα to mediate homeostasis. Accordingly, activation of AMPK rather than inhibition of IKKβ could substantially rescue LPS-induced mortality in IkkβC46A mice by rebuilding the homeostasis. We conclude that IKKβ activates AMPK to restrict inflammation and IKKβ mediates homeostatic function in inflammation via competitively phosphorylating AMPK and IκBα.
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Liu YC, Huang YT, Chen CJ. Development of a high-pH reversed-phase well plate for peptide fractionation and deep proteome analysis of cells and exosomes. Anal Bioanal Chem 2022; 414:2513-2522. [PMID: 35099582 DOI: 10.1007/s00216-022-03892-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/01/2022]
Abstract
The complexity of the proteome often limits the number of identified proteins in the nanoflow LC-MS (nanoLC-MS) analysis of samples. Therefore, peptide fractionation is essential for reducing the sample complexity and improving the proteome coverage. In this study, to achieve high-pH reversed-phase (RP)-well plate fractionation for high-throughput proteomics analysis, C18 particles were coated on a 96-well plate, and the sample-loading processes were optimized for high-pH fractionation. The sample capacity of the high-pH RP-well plate was estimated to be ~6 μg of protein. There were 1.85- and 1.71-fold increases in the number of protein groups and peptides identified, respectively, with high-pH RP-well plate fractionation, compared to those without fractionation. In addition, with alkaline C18 well plate fractionation, exosome markers could be detected using ~1 μg of a protein digest of exosomes by microflow LC-MS (microLC-MS). These results illustrate that high-pH RP-well plate fractionation has superior sensitivity and effectiveness in preparing trace amounts of proteins for deep proteome analysis.
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Affiliation(s)
- Yu-Ching Liu
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | | | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan. .,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
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5
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Gong S, Zhuo Y, Chen S, Hu X, Fan XX, Wu JL, Li N. Quantification of Osimertinib and Metabolite-Protein Modification Reveals Its High Potency and Long Duration of Effects on Target Organs. Chem Res Toxicol 2021; 34:2309-2318. [PMID: 34665607 DOI: 10.1021/acs.chemrestox.1c00195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent drugs are newly developed and proved to be successful therapies in past decades. However, the pharmacokinetics (PK) and pharmacodynamic (PD) studies of covalent drugs now ignore the drug and metabolite-protein modification. The low abundance of modified proteins also prevents its investigation. Herein, a simple, selective, and sensitive liquid chromatography-mass spectrometry (LC-MS)/MS quantitative method was established based on the mechanism of a drug and its metabolite-protein adducts using osimertinib as an example. Five metabolites with covalent modification potential were identified. The drug and its metabolite-cysteine adducts released from modified proteins by a mixed hydrolysis method were developed to characterize the level of the modified proteins. This turned the quantitative objects from proteins or peptides to small molecules, which increased the sensitivity and throughput of the quantitative approach. Accumulation of protein adducts formed by osimertinib and its metabolites in target organs was observed in vivo and long-lasting modifications were noted. These results interpreted the long duration of the covalent drugs' effect from the perspective of both parent and the metabolites. In addition, the established method could also be applied in blood testing as noninvasive monitoring. This newly developed approach showed great feasibility for PK and PD studies of covalent drugs.
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Affiliation(s)
- Shilin Gong
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Yue Zhuo
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China.,Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shengshuang Chen
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Xiaolan Hu
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Xing-Xing Fan
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Jian-Lin Wu
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Na Li
- Macau Institute for Applied Research in Medicine and Health, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China
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6
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LI J, ZHUO Y, ZHANG Y, LI N, WU J. [Size exclusion-reverse liquid column chromatography-mass spectrometry and its application in the identification of post-translationally modified proteins in rat kidney]. Se Pu 2021; 39:87-95. [PMID: 34227362 PMCID: PMC9274831 DOI: 10.3724/sp.j.1123.2020.05028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Proteomics is an emerging field that has been shown to play a crucial role in unveiling the mechanisms underlying physiological and pathological processes, and liquid chromatography-mass spectrometry (LC-MS) is one of the most important methods employed in this field. However, in complex biological systems, such as eukaryotes, it is challenging to perform a comprehensive and unbiased proteome analysis due to the high complexity of biological samples and enormous differences in sample contents. For example, post-translational modifications (PTMs) in proteins are imperative for cell signaling, but post-translationally modified proteins account for about 1% of the total proteins in a single cell, making their identification extremely difficult. Therefore, chromatographic separation methods based on different principles are generally applied to reduce the complexity of biological samples and enrich trace proteins for their identification through mass spectrometry (MS). In this study, we developed a new proteomics method by combining size exclusion chromatography (SEC) and reversed-phase chromatography (RPLC), to separate and identify trace proteins in complex systems. SEC was used to separate and enrich kidney-specific proteins. After optimization of the method, it was found that 30 mmol/L of ammonium acetate could efficiently separate rat kidney proteins from the total protein fraction so that they could be eluted based on their relative molecular mass. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis and LC-MS results showed that our SEC separation method not only refined the protein composition of the biological sample but also enhanced the relative contents of trace proteins through multiple injections. The collected protein fractions were further concentrated through ultrafiltration centrifugation followed by freeze-drying, which further improved the recovery of trace proteins by approximately 90% and largely decreased the time required with the use of freeze-drying alone. Thereafter, five protein fractions were separately digested using trypsin, and the resultant peptides were further analyzed by reverse phase chromatography-MS analysis. In the RPLC column, the peptides were isolated mainly based on their hydrophobicity. As a result, by combining SEC and RPLC, 23621 peptides and 1345 proteins were identified from the kidney, with an increase in numbers by 69% and 27%, respectively, when compared to those obtained using the common 2D strong cation exchange (SCX)-RPLC-MS method. However, no significant difference was observed in the pI and grand average of hydropathicity (GRAVY) values. Gene ontology (GO) analysis revealed an increase in the number of proteins in each cell component, especially the membrane. Furthermore, identification of a higher rate of identified peptides than proteins suggested that the protein coverage was also improved, thereby facilitating the detection of PTM proteins. Consequently, five common PTMs in biological processes, including methylation, acetylation, carbamylation, oxidation, and phosphorylation, were examined and compared between the two methods. As expected, the number of post-translationally modified peptides identified using SEC-RPLC-MS were 1.7-1.9 times more than those determined using the SCX-RPLC-MS method. Especially for the identification of phosphorylated peptides, we could achieve the level of the targeted enrichment strategy; however no significant difference was observed in the extents of phosphorylation among serine, threonine, and tyrosine. These results further indicate that upon combining SEC and RPLC, high efficiency could be achieved by decreasing the complexity of the protein sample, and the identification was unbiased. Finally, the phosphorylation of some kidney proteins, such as spectrin, L-lactate dehydrogenase, and ATPases, was found, which is critical for their functions. In summary, the SEC-RPLC-MS approach was developed for the identification of rat kidney proteins and is especially applicable for the identification of PTM proteins. Using this method, the identification efficiency for PTM peptides increased significantly. Therefore, this method has potential for better understanding the impact of PTM on kidney proteins and further elucidating the potential mechanisms underlying its physiological and pathological functions.
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Affiliation(s)
- Jianmin LI
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yue ZHUO
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yida ZHANG
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Na LI
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jianlin WU
- 澳门科技大学中医药学院, 中药质量研究国家重点实验室, 澳门 999078
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
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Zhang N, Liu X, Gao S, Wong CC. Parallel Channels-Multidimensional Protein Identification Technology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1440-1447. [PMID: 32310654 DOI: 10.1021/jasms.0c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Multidimensional protein identification (MudPIT), developed in the Yates Laboratory 20 years ago, is regarded as a powerful tool for proteomics research. Due to its remarkable online separation advantages, MudPIT has been widely used to facilitate discoveries in the field of proteomics research. However, it has one major disadvantage: the process of eluting peptides during strong cation exchange introduces salts, of different concentrations, into the mass spectrometer. Considering the sensitivity of the new generation of high-resolution mass spectrometers, developing a new version of MudPIT that could eliminate the introduction of salts in the elute would be a significant advancement to current technology. Herein, we developed a new, clean version of MudPIT called parallel channels-multidimensional protein identification technology (PC-MudPIT) to overcome this issue. In this design, the original biphasic trapping column was replaced by two parallel analytical column channels. We successfully averted the salt contamination yet retained all the other advantages of MudPIT. A total of 8161 and 7359 protein groups were identified from A549 whole cell lysate using PC-MudPIT and classic MudPIT, respectively. Moreover, we discovered the additional advantage that, in online mode, PC-MudPIT can also be used for an enrichment process of phosphopeptide identification. We identified a total 11453 phosphopeptides using PC-MudPIT and 7729 phosphopeptides using offline TiO2 enrichment followed by classic MudPIT. These advances indicate the possibility of other innovative applications of PC-MudPIT technology in deep proteome exploration.
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Affiliation(s)
- Nan Zhang
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shuaixin Gao
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
| | - Catherine Chiulan Wong
- Center for Precision Medicine Multi-omics Research, Peking University Health Science Center, Beijing 100191, China
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, China
- Peking University First Hosptal, Beijing 100034, China
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8
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Liu M, Li N, Zhang Y, Zheng Z, Zhuo Y, Sun B, Bai LP, Zhang M, Guo MQ, Wu JL. Characterization of covalent protein modification by triclosan in vivo and in vitro via three-dimensional liquid chromatography-mass spectrometry: New insight into its adverse effects. ENVIRONMENT INTERNATIONAL 2020; 136:105423. [PMID: 32035293 DOI: 10.1016/j.envint.2019.105423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/26/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Triclosan (TCS), an antimicrobial agent widely used in personal care products and ubiquitously exists in environment, has drawn increasing concern due to its potential to exert multiple adverse effects, ranging from endocrine disruption to carcinogenesis. However, the mechanism of these adverse effects is still not fully elucidated. More and more studies have shown that chemical reactive metabolites (RMs) covalently binding to proteins is a possible reason for these adverse effects, but there is still a lack of appropriate methods to predict or evaluate these adverse effects due to the extremely low abundance of the modified proteins in complex biological samples. In this study, we attempted to address this problem and investigate the possible mechanism of TCS adverse effects by a shotgun proteomics approach based on three-dimensional-liquid chromatography-mass spectrometry (3D-LC-MS). First, the in vitro incubation with model amino acids and protein in microsomes showed that TCS could react with cysteine residue of proteins through 3 types of RMs. Then, a 3D-LC-MS approach was developed to sensitively determine the low abundant modified proteins, which resulted in the identification of 45 TCS-modified proteins, including albumin, haptoglobin and NR1I2, in rats. STRING analysis indicated that these modified proteins mainly were involved in reproductive and development system, endocrine and immune system, and carcinogenesis, which were in accord with the main reported TCS-induced adverse effects and suggested that the covalent modification of TCS RMs for proteins might affect their activities and functions, thus inducing serious adverse effects. This study provided a new insight into the mechanism of TCS adverse effects and may serve as a valuable method to predict or evaluate adverse effects of ubiquitous chemicals.
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Affiliation(s)
- Meixian Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau.
| | - Yida Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
| | - Zhiyuan Zheng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
| | - Yue Zhuo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Center for Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau
| | - Mingming Zhang
- Department of Gastroenterology, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ming-Quan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau.
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9
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Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics. Int J Mol Sci 2020; 21:ijms21041524. [PMID: 32102244 PMCID: PMC7073195 DOI: 10.3390/ijms21041524] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.
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10
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van Pijkeren A, Bischoff R, Kwiatkowski M. Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture. Analyst 2019; 144:6812-6833. [PMID: 31650141 DOI: 10.1039/c9an01258c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.
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Affiliation(s)
- Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Dou M, Tsai CF, Piehowski PD, Wang Y, Fillmore TL, Zhao R, Moore RJ, Zhang P, Qian WJ, Smith RD, Liu T, Kelly RT, Shi T, Zhu Y. Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples. Anal Chem 2019; 91:9707-9715. [PMID: 31241912 DOI: 10.1021/acs.analchem.9b01248] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Chia-Feng Tsai
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Paul D Piehowski
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yang Wang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Pengfei Zhang
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Wei-Jun Qian
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Richard D Smith
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Tujin Shi
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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An B, Zhang M, Pu J, Shen S, Qu Y, Chen YJ, Huo S, Wang X, Polli JR, Balthasar JP, Herzog D, Ferrari L, Staack RF, Richter WF, Otteneder MB, Benincosa LJ, Zhou S, Vazvaei F, Qu J. High-Throughput, Sensitive LC-MS Quantification of Biotherapeutics and Biomarkers Using Antibody-Free, Peptide-Level, Multiple-Mechanism Enrichment via Strategic Regulation of pH and Ionic and Solvent Strengths. Anal Chem 2019; 91:3475-3483. [DOI: 10.1021/acs.analchem.8b05046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bo An
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Ming Zhang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Jie Pu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shichen Shen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yang Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Yuan-Ju Chen
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Shihan Huo
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xue Wang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Joseph Ryan Polli
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Joseph P. Balthasar
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Denis Herzog
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Luca Ferrari
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Roland F. Staack
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Munich, DE-82377 Penzberg, Germany
| | - Wolfgang F. Richter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Michael B. Otteneder
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Lisa J. Benincosa
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Shaolian Zhou
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Faye Vazvaei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center New York, New York, New York 10016, United States
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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Yuan H, Jiang B, Zhao B, Zhang L, Zhang Y. Recent Advances in Multidimensional Separation for Proteome Analysis. Anal Chem 2018; 91:264-276. [DOI: 10.1021/acs.analchem.8b04894] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Bo Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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Dou M, Chouinard CD, Zhu Y, Nagy G, Liyu AV, Ibrahim YM, Smith RD, Kelly RT. Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses. Anal Bioanal Chem 2018; 411:5363-5372. [PMID: 30397757 DOI: 10.1007/s00216-018-1452-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/09/2018] [Accepted: 10/24/2018] [Indexed: 10/27/2022]
Abstract
Mass spectrometry (MS)-based analysis of complex biological samples is essential for biomedical research and clinical diagnostics. The separation prior to MS plays a key role in the overall analysis, with separations having larger peak capacities often leading to more identified species and improved confidence in those identifications. High-resolution ion mobility (IM) separations enabled by Structures for Lossless Ion Manipulation (SLIM) can provide extremely rapid, high-resolution separations and are well suited as a second dimension of separation following nanoscale liquid chromatography (nanoLC). However, existing sample handling approaches for offline coupling of separation modes require microliter-fraction volumes and are thus not well suited for analysis of trace biological samples. We have developed a novel nanowell-mediated fractionation system that enables nanoLC-separated samples to be efficiently preconcentrated and directly infused at nanoelectrospray flow rates for downstream analysis. When coupled with SLIM IM-MS, the platform enables rapid and high-peak-capacity multidimensional separations of small biological samples. In this study, peptides eluting from a 100 nL/min nanoLC separation were fractionated into ~ 60 nanowells on a microfluidic glass chip using an in-house-developed robotic system. The dried samples on the chip were individually reconstituted and ionized by nanoelectrospray for SLIM IM-MS analysis. Using model peptides for characterization of the nanowell platform, we found that at least 80% of the peptide components of the fractionated samples were recovered from the nanowells, providing up to ~tenfold preconcentration for SLIM IM-MS analysis. The combined LC-SLIM IM separation peak capacities exceeded 3600 with a measurement throughput that is similar to current one-dimensional (1D) LC-MS proteomic analyses. Graphical abstract A nanowell-mediated multidimensional separation platform that combines nanoLC with SLIM IM-MS enables rapid, high-peak-capacity proteomic analyses.
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Affiliation(s)
- Maowei Dou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Christopher D Chouinard
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. .,Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
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15
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Zhu MZ, Chen GL, Wu JL, Li N, Liu ZH, Guo MQ. Recent development in mass spectrometry and its hyphenated techniques for the analysis of medicinal plants. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:365-374. [PMID: 29687660 DOI: 10.1002/pca.2763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/10/2018] [Accepted: 02/12/2018] [Indexed: 05/24/2023]
Abstract
INTRODUCTION Medicinal plants are gaining increasing attention worldwide due to their empirical therapeutic efficacy and being a huge natural compound pool for new drug discovery and development. The efficacy, safety and quality of medicinal plants are the main concerns, which are highly dependent on the comprehensive analysis of chemical components in the medicinal plants. With the advances in mass spectrometry (MS) techniques, comprehensive analysis and fast identification of complex phytochemical components have become feasible, and may meet the needs, for the analysis of medicinal plants. OBJECTIVE Our aim is to provide an overview on the latest developments in MS and its hyphenated technique and their applications for the comprehensive analysis of medicinal plants. METHODOLOGY Application of various MS and its hyphenated techniques for the analysis of medicinal plants, including but not limited to one-dimensional chromatography, multiple-dimensional chromatography coupled to MS, ambient ionisation MS, and mass spectral database, have been reviewed and compared in this work. RESULTS Recent advancs in MS and its hyphenated techniques have made MS one of the most powerful tools for the analysis of complex extracts from medicinal plants due to its excellent separation and identification ability, high sensitivity and resolution, and wide detection dynamic range. CONCLUSION To achieve high-throughput or multi-dimensional analysis of medicinal plants, the state-of-the-art MS and its hyphenated techniques have played, and will continue to play a great role in being the major platform for their further research in order to obtain insight into both their empirical therapeutic efficacy and quality control.
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Affiliation(s)
- Ming-Zhi Zhu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, P. R. China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Gui-Lin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
- The Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Jian-Lin Wu
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Taipa, Macau
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, P. R. China
| | - Ming-Quan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
- The Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, P. R. China
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Profiling of polyunsaturated fatty acids in human serum using off-line and on-line solid phase extraction-nano-liquid chromatography-quadrupole-time-of-flight mass spectrometry. J Chromatogr A 2018; 1537:141-146. [DOI: 10.1016/j.chroma.2018.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/03/2018] [Accepted: 01/07/2018] [Indexed: 01/16/2023]
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17
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Zhuo Y, Wu JL, Yan X, Guo MQ, Liu N, Zhou H, Liu L, Li N. Strategy for Hepatotoxicity Prediction Induced by Drug Reactive Metabolites Using Human Liver Microsome and Online 2D-Nano-LC-MS Analysis. Anal Chem 2017; 89:13167-13175. [DOI: 10.1021/acs.analchem.7b02684] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yue Zhuo
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Jian-Lin Wu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Xiaojing Yan
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
- Changzhou Affiliated Hospital of Nanjing University of Chinese Medicine, 25 Heping North Road, Changzhou 213003, China
| | - Ming-Quan Guo
- Key
Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,
Wuhan Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Ning Liu
- Central
Laboratory, Second Hospital of Jilin University, Changchun, China
| | - Hua Zhou
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Liang Liu
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
| | - Na Li
- State
Key Laboratory for Quality Research of Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macao
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