51
|
Zhang H, Lou C, Li J, Kang J. A gold foil covered fused silica capillary tip as a sheathless interface for coupling capillary electrophoresis-mass spectrometry. J Chromatogr A 2020; 1624:461215. [PMID: 32540065 DOI: 10.1016/j.chroma.2020.461215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
A method for the preparation of an on-column ESI emitter used as the sheathless interface for coupling capillary electrophoresis (CE) with mass spectrometry (MS) was developed. The emitter was directly fabricated at the outlet end of the separation capillary which was etched with HF solution to a symmetrical tip. The tip was covered with a small piece of gold foil which was fixed by epoxy resin glue for electrical contact. Such a prepared ESI emitter can produce a stable ESI signal over the wide range of flow rate from 50 nL/min to 800 nL/min. The performance of the CE-MS with the sheathless interface was evaluated by using the separation of four alkaloids. It was found that the strong electroosmotic flow produced by the multiple polyelectrolyte coating on the capillary is necessary for maintaining a stable MS signal. Effect of the running buffer composition, concentration and the CE separation voltages on the ESI signal strength were investigated. The absolute detection limits for the alkaloids was determined as fmol level. Moreover, the CE-MS was applied for the analyses of trypsin digestion of cytochrome C and small molecular organic anions. The emitter performed very stable with a lifetime of at least 180 h.
Collapse
Affiliation(s)
- Hanzhi Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; Shanghai Institute for Food and Drug Control, Zhangheng Road 1500, Shanghai 201203, China
| | - Chunli Lou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Jing Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China.
| |
Collapse
|
52
|
Zhou M, Uwugiaren N, Williams SM, Moore RJ, Zhao R, Goodlett D, Dapic I, Paša-Tolić L, Zhu Y. Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform. Anal Chem 2020; 92:7087-7095. [PMID: 32374172 DOI: 10.1021/acs.analchem.0c00467] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.
Collapse
Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Sarah M Williams
- 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
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland.,Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| |
Collapse
|
53
|
Chen D, Lubeckyj RA, Yang Z, McCool EN, Shen X, Wang Q, Xu T, Sun L. Predicting Electrophoretic Mobility of Proteoforms for Large-Scale Top-Down Proteomics. Anal Chem 2020; 92:3503-3507. [PMID: 32043875 PMCID: PMC7543059 DOI: 10.1021/acs.analchem.9b05578] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Large-scale top-down proteomics characterizes proteoforms in cells globally with high confidence and high throughput using reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) or capillary zone electrophoresis (CZE)-MS/MS. The false discovery rate (FDR) from the target-decoy database search is typically deployed to filter identified proteoforms to ensure high-confidence identifications (IDs). It has been demonstrated that the FDRs in top-down proteomics can be drastically underestimated. An alternative approach to the FDR can be useful for further evaluating the confidence of proteoform IDs after the database search. We argue that predicting retention/migration time of proteoforms from the RPLC/CZE separation accurately and comparing their predicted and experimental separation time could be a useful and practical approach. Based on our knowledge, there is still no report in the literature about predicting separation time of proteoforms using large top-down proteomics data sets. In this pilot study, for the first time, we evaluated various semiempirical models for predicting proteoforms' electrophoretic mobility (μef) using large-scale top-down proteomics data sets from CZE-MS/MS. We achieved a linear correlation between experimental and predicted μef of E. coli proteoforms (R2 = 0.98) with a simple semiempirical model, which utilizes the number of charges and molecular mass of each proteoform as the parameters. Our modeling data suggest that the complete unfolding of proteoforms during CZE separation benefits the prediction of their μef. Our results also indicate that N-terminal acetylation and phosphorylation both decrease the proteoforms' charge by roughly one charge unit.
Collapse
Affiliation(s)
- Daoyang Chen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
54
|
Kristoff CJ, Li C, Li P, Holland LA. Low Flow Voltage Free Interface for Capillary Electrophoresis and Mass Spectrometry Driven by Vibrating Sharp-Edge Spray Ionization. Anal Chem 2020; 92:3006-3013. [PMID: 31971372 PMCID: PMC7295075 DOI: 10.1021/acs.analchem.9b03994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Capillary electrophoresis-mass spectrometry is a powerful technique for high-throughput and high efficiency separations combined with structural identification. Electrospray ionization is the primary interface used to couple capillary electrophoresis to mass analyzers; however, improved designs continue to be reported. A new interfacing method based on vibrating sharp-edge spray ionization is presented in this work to overcome the challenges of decoupling applied voltages and to enhance the compatibility with separations performed at near-neutral pH. The versatility and ease of use of this ionization source is demonstrated using β-blockers, peptides, and proteins. The cationic β-blocker pindolol was injected electrokinetically, and detected at concentrations ranging from 10 nM to 5 μM, with an estimated detection limit of 2 nM. The vibrating sharp-edge spray ionization functions with flow rates from 70 to 200 nL/min and did not perturb the capillary electrophoresis separation electroosmotic flow as evidenced by the observation that most migration times differed less than 7% (n = 3) across a lab-built system interfaced to mass spectrometry and a commercial system that utilizes absorbance detection. For cationic beta-blockers the theoretical plates achieved in the capillary electrophoresis-mass spectrometry setup were 80%-95% of that observed with a commercial capillary electrophoresis-UV absorbance detection system.
Collapse
Affiliation(s)
- Courtney J. Kristoff
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lisa A. Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| |
Collapse
|
55
|
Abstract
Top-down mass spectrometry (MS) analyzes intact proteins at the proteoform level, which allows researchers to better understand the functions of protein modifications. Recently, top-down proteomics has increased in popularity due to advancements in high-resolution mass spectrometers, increased efficiency in liquid chromatography (LC) separation, and advances in data analysis software. Some unique protein proteoforms, which have been distinguished using top-down MS, have even been shown to exhibit marked variation in biological function compared to similar proteoforms. However, the qualitative identification of a particular proteoform may not be enough to determine the biological relevance of that proteoform. Quantitative top-down MS methods have been notably applied to the study of the differing biological functions of protein proteoforms and have allowed researchers to explore proteomes at the proteoform, rather than the peptide, level. Here, we review the top-down MS methods that have been used to quantitatively identify intact proteins, discuss current applications of quantitative top-down MS analysis, and present new areas where quantitative top-down MS analysis may be implemented.
Collapse
Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK 73019-5251, USA.
| | | |
Collapse
|
56
|
Kristoff CJ, Bwanali L, Veltri LM, Gautam GP, Rutto PK, Newton EO, Holland LA. Challenging Bioanalyses with Capillary Electrophoresis. Anal Chem 2020; 92:49-66. [PMID: 31698907 PMCID: PMC6995690 DOI: 10.1021/acs.analchem.9b04718] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Courtney J. Kristoff
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lindsay M. Veltri
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Gayatri P. Gautam
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Patrick K. Rutto
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Ebenezer O. Newton
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lisa A. Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| |
Collapse
|
57
|
Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
58
|
Yu D, Wang Z, Cupp-Sutton KA, Liu X, Wu S. Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2502-2513. [PMID: 31755044 PMCID: PMC7539543 DOI: 10.1007/s13361-019-02315-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 08/10/2019] [Accepted: 08/10/2019] [Indexed: 05/26/2023]
Abstract
Post-translational modifications (PTMs) play critical roles in biological processes and have significant effects on the structures and dynamics of proteins. Top-down proteomics methods were developed for and applied to the study of intact proteins and their PTMs in human samples. However, the large dynamic range and complexity of human samples makes the study of human proteins challenging. To address these challenges, we developed a 2D pH RP/RPLC-MS/MS technique that fuses high-resolution separation and intact protein characterization to study the human proteins in HeLa cell lysate. Our results provide a deep coverage of soluble proteins in human cancer cells. Compared to 225 proteoforms from 124 proteins identified when 1D separation was used, 2778 proteoforms from 628 proteins were detected and characterized using our 2D separation method. Many proteoforms with critically functional PTMs including phosphorylation were characterized. Additionally, we present the first detection of intact human GcvH proteoforms with rare modifications such as octanoylation and lipoylation. Overall, the increase in the number of proteoforms identified using 2DLC separation is largely due to the reduction in sample complexity through improved separation resolution, which enables the detection of low-abundance PTM-modified proteoforms. We demonstrate here that 2D pH RP/RPLC is an effective technique to analyze complex protein samples using top-down proteomics.
Collapse
Affiliation(s)
- Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA
| | - Xiaowen Liu
- School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019-5251, USA.
| |
Collapse
|
59
|
McCool EN, Lodge JM, Basharat AR, Liu X, Coon JJ, Sun L. Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2470-2479. [PMID: 31073891 PMCID: PMC6527361 DOI: 10.1007/s13361-019-02206-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 05/21/2023]
Abstract
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as an efficient approach for top-down proteomics recently for its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based dissociation methods often cannot provide extensive fragmentation of proteoforms for thorough characterization. Activated ion electron transfer dissociation (AI-ETD), that combines infrared photoactivation concurrent with ETD, has shown better performance for proteoform fragmentation than higher energy-collisional dissociation (HCD) and standard ETD. Here, we present the first application of CZE-AI-ETD on an Orbitrap Fusion Lumos mass spectrometer for large-scale top-down proteomics of Escherichia coli (E. coli) cells. CZE-AI-ETD outperformed CZE-ETD regarding proteoform and protein identifications (IDs). CZE-AI-ETD reached comparable proteoform and protein IDs with CZE-HCD. CZE-AI-ETD tended to generate better expectation values (E values) of proteoforms than CZE-HCD and CZE-ETD, indicating a higher quality of MS/MS spectra from AI-ETD respecting the number of sequence-informative fragment ions generated. CZE-AI-ETD showed great reproducibility regarding the proteoform and protein IDs with relative standard deviations less than 4% and 2% (n = 3). Coupling size exclusion chromatography (SEC) to CZE-AI-ETD identified 3028 proteoforms and 387 proteins from E. coli cells with 1% spectrum level and 5% proteoform-level false discovery rates. The data represents the largest top-down proteomics dataset using the AI-ETD method so far. Single-shot CZE-AI-ETD of one SEC fraction identified 957 proteoforms and 253 proteins. N-terminal truncations, signal peptide cleavage, N-terminal methionine removal, and various post-translational modifications including protein N-terminal acetylation, methylation, S-thiolation, disulfide bonds, and lysine succinylation were detected.
Collapse
Affiliation(s)
- Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Jean M Lodge
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Avenue, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN, 46202, USA
| | - Joshua J Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
| |
Collapse
|
60
|
Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2017–mid 2019). Electrophoresis 2019; 41:10-35. [DOI: 10.1002/elps.201900269] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/08/2019] [Accepted: 10/19/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Prague 6 Czechia
| |
Collapse
|
61
|
Gomes FP, Yates JR. Recent trends of capillary electrophoresis-mass spectrometry in proteomics research. MASS SPECTROMETRY REVIEWS 2019; 38:445-460. [PMID: 31407381 PMCID: PMC6800771 DOI: 10.1002/mas.21599] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Progress in proteomics research has led to a demand for powerful analytical tools with high separation efficiency and sensitivity for confident identification and quantification of proteins, posttranslational modifications, and protein complexes expressed in cells and tissues. This demand has significantly increased interest in capillary electrophoresis-mass spectrometry (CE-MS) in the past few years. This review provides highlights of recent advances in CE-MS for proteomics research, including a short introduction to top-down mass spectrometry and native mass spectrometry (native MS), as well as a detailed overview of CE methods. Both the potential and limitations of these methods for the analysis of proteins and peptides in synthetic and biological samples and the challenges of CE methods are discussed, along with perspectives about the future direction of CE-MS. @ 2019 Wiley Periodicals, Inc. Mass Spec Rev 00:1-16, 2019.
Collapse
Affiliation(s)
| | - John R. Yates
- Correspondent author: , Phone number: (858) 784-8862, Departments of Molecular Medicine and Neurobiology, 10550 North Torrey Pines Road, SR302B, The Scripps Research Institute, La Jolla, CA 92037
| |
Collapse
|
62
|
Shen X, Yang Z, McCool EN, Lubeckyj RA, Chen D, Sun L. Capillary zone electrophoresis-mass spectrometry for top-down proteomics. Trends Analyt Chem 2019; 120:115644. [PMID: 31537953 PMCID: PMC6752746 DOI: 10.1016/j.trac.2019.115644] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS)-based top-down proteomics characterizes complex proteomes at the intact proteoform level and provides an accurate picture of protein isoforms and protein post-translational modifications in the cell. The progress of top-down proteomics requires novel analytical tools with high peak capacity for proteoform separation and high sensitivity for proteoform detection. The requirements have made capillary zone electrophoresis (CZE)-MS an attractive approach for advancing large-scale top-down proteomics. CZE has achieved a peak capacity of 300 for separation of complex proteoform mixtures. CZE-MS has shown drastically better sensitivity than commonly used reversed-phase liquid chromatography (RPLC)-MS for proteoform detection. The advanced CZE-MS identified 6,000 proteoforms of nearly 1,000 proteoform families from a complex proteome sample, which represents one of the largest top-down proteomic datasets so far. In this review, we focus on the recent progress in CZE-MS-based top-down proteomics and provide our perspectives about its future directions.
Collapse
Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Rachele A. Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
63
|
Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level. Proteomes 2019; 7:proteomes7040036. [PMID: 31671630 PMCID: PMC6958347 DOI: 10.3390/proteomes7040036] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/15/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (Mr). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and Mr. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.
Collapse
|
64
|
Yang Z, Shen X, Chen D, Sun L. Improved Nanoflow RPLC-CZE-MS/MS System with High Peak Capacity and Sensitivity for Nanogram Bottom-up Proteomics. J Proteome Res 2019; 18:4046-4054. [PMID: 31610113 DOI: 10.1021/acs.jproteome.9b00545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Novel mass spectrometry (MS)-based proteomic tools with extremely high sensitivity and high peak capacity are required for comprehensive characterization of protein molecules in mass-limited samples. We reported a nanoRPLC-CZE-MS/MS system for deep bottom-up proteomics of low micrograms of human cell samples in previous work. In this work, we improved the sensitivity of the nanoRPLC-CZE-MS/MS system drastically via employing bovine serum albumin (BSA)-treated sample vials, improving the nanoRPLC fraction collection procedure, and using a short capillary for fast CZE separation. The improved nanoRPLC-CZE produced a peak capacity of 8500 for peptide separation. The improved system identified 6500 proteins from a MCF7 proteome digest starting with only 500 ng of peptides using a Q-Exactive HF mass spectrometer. The system produced a comparable number of protein identifications (IDs) to our previous system and the two-dimensional (2D) nanoRPLC-MS/MS system developed by Mann's group with 10-fold and 4-fold less sample consumption, respectively. We coupled the single-spot solid phase sample preparation (SP3) method to the improved nanoRPLC-CZE-MS/MS for bottom-up proteomics of 5000 HEK293T cells, resulting in 3689 protein IDs with the consumption of a peptide amount that corresponded to only roughly 1000 cells.
Collapse
Affiliation(s)
- Zhichang Yang
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Xiaojing Shen
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Daoyang Chen
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Liangliang Sun
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| |
Collapse
|
65
|
[Comparing nanoflow reversed-phase liquid chromatography-tandem mass spectrometry and capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics]. Se Pu 2019; 37:878-886. [PMID: 31642259 DOI: 10.3724/sp.j.1123.2019.05001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
One of the major shortcomings in top-down proteomics is the lack of efficient separations for intact proteins that can be effectively coupled to mass spectrometry. Capillary zone electrophoresis (CZE) and nanoflow reversed-phase liquid chromatography (nanoRPLC) are two methods that can be coupled to mass spectrometry directly and have been recently advanced in terms of their ability to separate intact proteins in complex biological mixtures. In this work, for the first time, we compared the state-of-the-art nanoRPLC-MS/MS and CZE-MS/MS platforms for top-down characterization of a standard protein mixture and an Escherichia coli (E. coli) proteome sample. CZE-MS produced comparable signals of standard proteins to RPLC-MS with 10-times less sample consumption. Interestingly, the proteins in RPLC-MS tended to have higher charge states than in CZE-MS, most likely due to the high acetonitrile concentration in RPLC mobile phase, leading to the more extensive unfolding of proteins in RPLC compared to in CZE. CZE-MS/MS identified 159 proteins and 513 proteoforms using 1-μg E. coli proteins in a single run and outperformed RPLC-MS/MS using 1-μg E. coli proteins in terms of protein and proteoform identifications (159 vs. 105 proteins and 513 vs. 277 proteoforms). The RPLC-MS/MS using 8-μg E. coli proteins identified 245 proteins and 1004 proteoforms in a single run, and the data was much better than that from CZE-MS/MS (1-μg E. coli proteins) regarding the number of identifications because of the 8-times higher sample loading amount and significantly wider separation window of RPLC-MS/MS compared to CZE-MS/MS.
Collapse
|
66
|
Lubeckyj RA, Basharat AR, Shen X, Liu X, Sun L. Large-Scale Qualitative and Quantitative Top-Down Proteomics Using Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry with Nanograms of Proteome Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1435-1445. [PMID: 30972727 PMCID: PMC6675661 DOI: 10.1007/s13361-019-02167-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has attracted attention recently for top-down proteomics because it can achieve highly efficient separation and very sensitive detection of proteins. However, separation window and sample loading volume of CZE need to be boosted for a better proteome coverage using CZE-MS/MS. Here, we present an improved CZE-MS/MS system that achieved a 180-min separation window and a 2-μL sample loading volume for top-down characterization of protein mixtures. The system obtained highly efficient separation of proteins with nearly one million theoretical plates for myoglobin and enabled baseline separation of three different proteoforms of myoglobin. The CZE-MS/MS system identified 797 ± 21 proteoforms and 258 ± 7 proteins (n = 2) from an Escherichia coli (E. coli) proteome sample in a single run with only 250 ng of proteins injected. The system still identified 449 ± 40 proteoforms and 173 ± 6 proteins (n = 2) from the E. coli sample when only 25 ng of proteins were injected per run. Single-shot CZE-MS/MS analyses of zebrafish brain cerebellum (Cb) and optic tectum (Teo) regions identified 1730 ± 196 proteoforms (n = 3) and 2024 ± 255 proteoforms (n = 3), respectively, with only 500-ng proteins loaded per run. Label-free quantitative top-down proteomics of zebrafish brain Cb and Teo regions revealed significant differences between Cb and Teo regarding the proteoform abundance. Over 700 proteoforms from 131 proteins had significantly higher abundance in Cb compared to Teo, and these proteins were highly enriched in several biological processes, including muscle contraction, glycolytic process, and mesenchyme migration. Graphical Abstract.
Collapse
Affiliation(s)
- Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI, 48824, USA.
| |
Collapse
|
67
|
|
68
|
McCool EN, Chen D, Li W, Liu Y, Sun L. Capillary zone electrophoresis-tandem mass spectrometry using ultraviolet photodissociation (213 nm) for large-scale top-down proteomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2019; 11:2855-2861. [PMID: 31608127 PMCID: PMC6788745 DOI: 10.1039/c9ay00585d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has attracted attention recently for large-scale top-down proteomics that aims to characterize proteoforms in cells at a global scale and with high throughput. In this work, CZE-MS/MS with ultraviolet photodissociation (UVPD) was evaluated for large-scale top-down proteomics for the first time. Roughly, 600 proteoforms and 369 proteins were identified from a zebrafish brain sample via coupling size exclusion chromatography (SEC) fractionation to CZE-UVPD. The dataset represents one of the largest top-down proteomics datasets using UVPD. Single-shot CZE-UVPD identified 227 proteoforms of 139 proteins from one SEC fraction of the zebrafish brain sample. The SEC-CZE-UVPD system identified zebrafish brain proteoforms in a mass range of 3-21 kDa. The UVPD with 213-nm photons produced reasonably good gas-phase fragmentation of proteoforms. For instance, 75% backbone cleavages were observed for Parvalbumin-7 with about 12-kDa molecular weight. The system detected various post-translational modifications (PTMs) from the zebrafish brain sample, including N-terminal acetylation, trimethylation and myristoylation of N-terminal glycine. Two different proteoforms of calmodulin, with either only N-terminal acetylation or both N-terminal acetylation and K115 trimethylation, were identified in the zebrafish brain sample. To our best knowledge, there is no experimental evidence reported in the literature on the two proteoforms of calmodulin in the zebrafish brain.
Collapse
Affiliation(s)
- Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wenxue Li
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, CT 06516, United States
| | - Yansheng Liu
- Department of Pharmacology, Cancer Biology Institute, Yale University School of Medicine, West Haven, CT 06516, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
- Corresponding author. , Phone: 1-517-353-0498
| |
Collapse
|
69
|
Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics 2019; 19:e1800361. [PMID: 31050378 PMCID: PMC6602557 DOI: 10.1002/pmic.201800361] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/07/2019] [Indexed: 12/29/2022]
Abstract
A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.
Collapse
Affiliation(s)
- Leah V Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Neil L Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry and Molecular Biosciences and the Division of Hematology and Oncology, Northwestern University, Evanston, IL, 60208, USA
| | - Richard D LeDuc
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT, 84602
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M Thomas
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dahang Yu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
70
|
Wang T, Chen D, Lubeckyj RA, Shen X, Yang Z, McCool EN, Qiao X, Sun L. Capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics using attapulgite nanoparticles functionalized separation capillaries. Talanta 2019; 202:165-170. [PMID: 31171165 DOI: 10.1016/j.talanta.2019.04.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
Attapulgite nanoparticles have good chemical properties and can be modified easily for broad applications. In this work, for the first time, attapulgite nanoparticles were employed to modify the inner wall of separation capillaries for capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS)-based top-down proteomics. The attapulgite nanoparticles and the inner wall of a fused silica capillary were first functionalized with γ-methacryloxypropyl trimethoxysilane. Then the modified nanoparticles and acrylamide were copolymerized in the fused silica capillary with the assistance of azobisisobutyronitrile and heat. The incorporation of high-surface-area nanoparticles in the linear polyacrylamide (LPA) coating resulted in significantly lower electroosmotic mobility compared with the typical LPA coating (3.48 × 10-5 vs. 9.03 × 10-5 cm2 V-1 S-1), most likely because more LPA molecules were immobilized on the inner wall of the separation capillary. The attapulgite nanoparticles functionalized separation capillaries have shown great stability and reproducibility across 43 discontinuous CZE-MS runs of a standard protein mixture. We applied the CZE-MS/MS system for top-down proteomics of Escherichia coli cells. In a proof-of-principle experiment, the CZE-MS/MS system achieved a 90-min separation window and a 1-μL sample loading volume, leading to nearly 300 proteoform and 135 protein identifications in a single run. Many post-translational modifications (PTMs) were identified, including methylation, acetylation, phosphorylation, biotinylation, succinylation, and disulfide bond.
Collapse
Affiliation(s)
- Tingting Wang
- School of Materials and Chemical Engineering, Ningbo University of Technology, Ningbo 315211, China; Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Rachele A Lubeckyj
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Elijah N McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA
| | - Xiaoqiang Qiao
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA; College of Pharmaceutical Sciences, Key Laboratory of Analytical Science and Technology of Hebei Province, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding 071002, China
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824, USA.
| |
Collapse
|
71
|
Tucholski T, Knott SJ, Chen B, Pistono P, Lin Z, Ge Y. A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2019; 91:3835-3844. [PMID: 30758949 DOI: 10.1021/acs.analchem.8b04082] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry (MS) based top-down proteomics provides rich information about proteoforms arising from combinatorial amino acid sequence variations and post-translational modifications (PTMs). Fourier transform ion cyclotron resonance (FT-ICR) MS affords ultrahigh resolving power and provides high-accuracy mass measurements, presenting a powerful tool for top-down MS characterization of proteoforms. However, the detection and characterization of large proteins from complex mixtures remain challenging due to the exponential decrease in S: N with increasing molecular weight (MW) and coeluting low-MW proteins; thus, size-based fractionation of complex protein mixtures prior to MS analysis is necessary. Here, we directly combine MS-compatible serial size exclusion chromatography (sSEC) fractionation with 12 T FT-ICR MS for targeted top-down characterization of proteins from complex mixtures extracted from human and swine heart tissue. Benefiting from the ultrahigh resolving power of FT-ICR, we isotopically resolved 31 distinct proteoforms (30-50 kDa) simultaneously in a single mass spectrum within a 100 m/ z window. Notably, within a 5 m/ z window, we obtained baseline isotopic resolution for 6 distinct large proteoforms (30-50 kDa). The ultrahigh resolving power of FT-ICR MS combined with sSEC fractionation enabled targeted top-down analysis of large proteoforms (>30 kDa) from the human heart proteome without extensive chromatographic separation or protein purification. Further separation of proteoforms inside the mass spectrometer (in-MS) allowed for isolation of individual proteoforms and targeted electron capture dissociation (ECD), yielding high sequence coverage. sSEC/FT-ICR ECD facilitated the identification and sequence characterization of important metabolic enzymes. This platform, which facilitates deep interrogation of proteoform primary structure, is highly tunable, allows for adjustment of MS and MS/MS parameters in real time, and can be utilized for a variety of complex protein mixtures.
Collapse
Affiliation(s)
- Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Samantha J Knott
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paige Pistono
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
| |
Collapse
|
72
|
Capriotti AL, Cavaliere C, Piovesana S. Liposome protein corona characterization as a new approach in nanomedicine. Anal Bioanal Chem 2019; 411:4313-4326. [DOI: 10.1007/s00216-019-01656-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/07/2019] [Accepted: 01/30/2019] [Indexed: 11/27/2022]
|
73
|
Liang Y, Jin Y, Wu Z, Tucholski T, Brown KA, Zhang L, Zhang Y, Ge Y. Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics. Anal Chem 2019; 91:1743-1747. [PMID: 30668094 DOI: 10.1021/acs.analchem.8b05817] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Top-down mass spectrometry (MS)-based proteomics has become a powerful tool for comprehensive characterization of intact proteins. However, because of the high complexity of the proteome, highly effective separation of intact proteins from complex mixtures prior to MS analysis remains challenging. Monolithic columns have shown great promise for intact protein separation due to their high permeability, low backpressure, and fast mass transfer. Herein, for the first time, we developed bridged hybrid bis(triethoxysilyl)ethylene (BTSEY) monolith with C8 functional groups (C8@BTSEY) for highly effective protein separation and coupled it to high-resolution MS for identification of intact proteins from complex protein mixtures. We have optimized mobile phase conditions of our monolith-based reverse-phase chromatography (RPC) for online liquid chromatography (LC)-MS analysis and evaluated separation reproducibility of the C8@BTSEY column. We further assessed the chromatographic performance of this column by separating a complex protein mixture extracted from swine heart tissue. Using our monolithic column (i.d. 100 μm × 35 cm), we separated over 300 proteoforms (up to 104 kDa) from 360 ng of protein mixture in an 80 min one-dimensional (1D) LC run. The highly effective separation and recovery of intact proteins from this monolithic column allowed unambiguous identification of ∼100 proteoforms including a large protein, αactinin2 (103.77 kDa), by online 1D LC-MS/MS analysis for the first time. As demonstrated, this C8@BTSEY column is reproducible and effective in separation of intact proteins, which shows high promise for top-down proteomics.
Collapse
Affiliation(s)
- Yu Liang
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yutong Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Zhijie Wu
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Kyle A Brown
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , Liaoning 116023 , China
| | - Ying Ge
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program, School of Medicine and Public Health , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| |
Collapse
|
74
|
Štěpánová S, Kašička V. Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018). J Sep Sci 2018; 42:398-414. [DOI: 10.1002/jssc.201801090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; The Czech Academy of Sciences; Prague 6 Czechia
| |
Collapse
|
75
|
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: 4.3] [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
| |
Collapse
|
76
|
Stolz A, Jooß K, Höcker O, Römer J, Schlecht J, Neusüß C. Recent advances in capillary electrophoresis-mass spectrometry: Instrumentation, methodology and applications. Electrophoresis 2018; 40:79-112. [PMID: 30260009 DOI: 10.1002/elps.201800331] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
Abstract
Capillary electrophoresis (CE) offers fast and high-resolution separation of charged analytes from small injection volumes. Coupled to mass spectrometry (MS), it represents a powerful analytical technique providing (exact) mass information and enables molecular characterization based on fragmentation. Although hyphenation of CE and MS is not straightforward, much emphasis has been placed on enabling efficient ionization and user-friendly coupling. Though several interfaces are now commercially available, research on more efficient and robust interfacing with nano-electrospray ionization (ESI), matrix-assisted laser desorption/ionization (MALDI) and inductively coupled plasma mass spectrometry (ICP) continues with considerable results. At the same time, CE-MS has been used in many fields, predominantly for the analysis of proteins, peptides and metabolites. This review belongs to a series of regularly published articles, summarizing 248 articles covering the time between June 2016 and May 2018. Latest developments on hyphenation of CE with MS as well as instrumental developments such as two-dimensional separation systems with MS detection are mentioned. Furthermore, applications of various CE-modes including capillary zone electrophoresis (CZE), nonaqueous capillary electrophoresis (NACE), capillary gel electrophoresis (CGE) and capillary isoelectric focusing (CIEF) coupled to MS in biological, pharmaceutical and environmental research are summarized.
Collapse
Affiliation(s)
| | - Kevin Jooß
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Oliver Höcker
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Instrumental Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jennifer Römer
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany
| | - Johannes Schlecht
- Faculty of Chemistry, Aalen University, Aalen, Germany.,Department of Pharmaceutical/Medicinal Chemistry, Friedrich Schiller University, Jena, Germany
| | | |
Collapse
|
77
|
Breadmore MC, Grochocki W, Kalsoom U, Alves MN, Phung SC, Rokh MT, Cabot JM, Ghiasvand A, Li F, Shallan AI, Keyon ASA, Alhusban AA, See HH, Wuethrich A, Dawod M, Quirino JP. Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2016-2018). Electrophoresis 2018; 40:17-39. [PMID: 30362581 DOI: 10.1002/elps.201800384] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022]
Abstract
One of the most cited limitations of capillary and microchip electrophoresis is the poor sensitivity. This review continues to update this series of biannual reviews, first published in Electrophoresis in 2007, on developments in the field of online/in-line concentration methods in capillaries and microchips, covering the period July 2016-June 2018. It includes developments in the field of stacking, covering all methods from field-amplified sample stacking and large-volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to online or in-line extraction methods that have been used for electrophoresis.
Collapse
Affiliation(s)
- Michael C Breadmore
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia
| | - Wojciech Grochocki
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia.,Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Umme Kalsoom
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia.,ARC Centre of Excellence for Electromaterials Science (ACES), School of Natural Sciences, College of Science and Technology, University of Tasmania, Hobart, Australia
| | - Mónica N Alves
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia
| | - Sui Ching Phung
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Joan M Cabot
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia.,ARC Centre of Excellence for Electromaterials Science (ACES), School of Natural Sciences, College of Science and Technology, University of Tasmania, Hobart, Australia
| | - Alireza Ghiasvand
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia.,Department of Chemistry, Lorestan University, Khoramabad, Iran
| | - Feng Li
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia
| | - Aliaa I Shallan
- Future Industries Institute (FII), University of South Australia, Mawson Lakes, Australia.,Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Aemi S Abdul Keyon
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia.,Centre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Ala A Alhusban
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Hong Heng See
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia.,Centre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
| | - Alain Wuethrich
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia
| | - Mohamed Dawod
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Joselito P Quirino
- Australian Centre for Research on Separation Science, Chemistry, School of Natural Science, University of Tasmania, Hobart, Tasmania, Australia
| |
Collapse
|
78
|
|
79
|
McCool EN, Lubeckyj R, Shen X, Kou Q, Liu X, Sun L. Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry. J Vis Exp 2018. [PMID: 30417888 DOI: 10.3791/58644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down proteomics that aims to characterize proteoforms in complex proteomes. However, the application of CZE-MS/MS for large-scale top-down proteomics has been impeded by the low sample-loading capacity and narrow separation window of CZE. Here, a protocol is described using CZE-MS/MS with a microliter-scale sample-loading volume and a 90-min separation window for large-scale top-down proteomics. The CZE-MS/MS platform is based on a linear polyacrylamide (LPA)-coated separation capillary with extremely low electroosmotic flow, a dynamic pH-junction-based online sample concentration method with a high efficiency for protein stacking, an electro-kinetically pumped sheath flow CE-MS interface with extremely high sensitivity, and an ion trap mass spectrometer with high mass resolution and scan speed. The platform can be used for the high-resolution characterization of simple intact protein samples and the large-scale characterization of proteoforms in various complex proteomes. As an example, a highly efficient separation of a standard protein mixture and a highly sensitive detection of many impurities using the platform is demonstrated. As another example, this platform can produce over 500 proteoform and 190 protein identifications from an Escherichia coli proteome in a single CZE-MS/MS run.
Collapse
Affiliation(s)
| | | | | | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine
| | | |
Collapse
|
80
|
Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. J Proteome Res 2018; 17:3526-3536. [PMID: 30180576 PMCID: PMC6201694 DOI: 10.1021/acs.jproteome.8b00469] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of effective strategies for the comprehensive identification and quantification of proteoforms in complex systems is a critical challenge in proteomics. Proteoforms, the specific molecular forms in which proteins are present in biological systems, are the key effectors of biological function. Thus, knowledge of proteoform identities and abundances is essential to unraveling the mechanisms that underlie protein function. We recently reported a strategy that integrates conventional top-down mass spectrometry with intact-mass determinations for enhanced proteoform identifications and the elucidation of proteoform families and applied it to the analysis of yeast cell lysate. In the present work, we extend this strategy to enable quantification of proteoforms, and we examine changes in the abundance of murine mitochondrial proteoforms upon differentiation of mouse myoblasts to myotubes. The integrated top-down and intact-mass strategy provided an increase of ∼37% in the number of identified proteoforms compared to top-down alone, which is in agreement with our previous work in yeast; 1779 unique proteoforms were identified using the integrated strategy compared to 1301 using top-down analysis alone. Quantitative comparison of proteoform differences between the myoblast and myotube cell types showed 129 observed proteoforms exhibiting statistically significant abundance changes (fold change >2 and false discovery rate <5%).
Collapse
Affiliation(s)
- Leah V. Schaffer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Michael R. Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anthony J. Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian L. Frey
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J. Pagliarini
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
81
|
Yang Z, Shen X, Chen D, Sun L. Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom-Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest. Anal Chem 2018; 90:10479-10486. [PMID: 30102516 PMCID: PMC6156779 DOI: 10.1021/acs.analchem.8b02466] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains, or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least 500 μg of complex proteome digests were required for the LC/CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples. In this work, we coupled microscale reversed-phase LC (μRPLC)-based peptide prefractionation to dynamic pH-junction-based CZE-MS/MS for deep bottom-up proteomics of the MCF7 breast cancer cell proteome starting with only 5 μg of peptides. The dynamic pH-junction-based CZE enabled a 500 nL sample injection from as low as a 1.5 μL peptide sample, using up to 33% of the available peptide material for an analysis. Two kinds of μRPLC prefractionation were investigated, C18 ZipTip and nanoflow RPLC. C18 ZipTip/CZE-MS/MS identified 4453 proteins from 5 μg of the MCF7 proteome digest and showed good qualitative and quantitative reproducibility. Nanoflow RPLC/CZE-MS/MS produced over 7500 protein IDs and nearly 60 000 peptide IDs from the 5 μg of MCF7 proteome digest. The nanoflow RPLC/CZE-MS/MS platform reduced the required amount of complex proteome digests for LC/CZE-MS/MS-based deep bottom-up proteomics by 2 orders of magnitude. Our work provides the proteomics community with a powerful tool for deep and highly sensitive proteomics.
Collapse
Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| |
Collapse
|
82
|
Shen X, Kou Q, Guo R, Yang Z, Chen D, Liu X, Hong H, Sun L. Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry. Anal Chem 2018; 90:10095-10099. [PMID: 30085653 PMCID: PMC6156775 DOI: 10.1021/acs.analchem.8b02725] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Native proteomics aims to characterize complex proteomes under native conditions and ultimately produces a full picture of endogenous protein complexes in cells. It requires novel analytical platforms for high-resolution and liquid-phase separation of protein complexes prior to native mass spectrometry (MS) and MS/MS. In this work, size-exclusion chromatography (SEC)-capillary zone electrophoresis (CZE)-MS/MS was developed for native proteomics in discovery mode, resulting in the identification of 144 proteins, 672 proteoforms, and 23 protein complexes from the Escherichia coli proteome. The protein complexes include four protein homodimers, 16 protein-metal complexes, two protein-[2Fe-2S] complexes, and one protein-glutamine complex. Half of them have not been reported in the literature. This work represents the first example of online liquid-phase separation-MS/MS for the characterization of a complex proteome under the native condition, offering the proteomics community an efficient and simple platform for native proteomics.
Collapse
Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Qiang Kou
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
| | - Ruiqiong Guo
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN 46202 USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| |
Collapse
|
83
|
Calvete JJ. Snake venomics – from low-resolution toxin-pattern recognition to toxin-resolved venom proteomes with absolute quantification. Expert Rev Proteomics 2018; 15:555-568. [DOI: 10.1080/14789450.2018.1500904] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, CSIC, Valencia, Spain
| |
Collapse
|
84
|
Employing proteomics to understand the effects of nutritional intervention in cancer treatment. Anal Bioanal Chem 2018; 410:6371-6386. [PMID: 29974151 DOI: 10.1007/s00216-018-1219-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 12/22/2022]
Abstract
Lifestyle optimizations are implementable changes that can have an impact on health and disease. Nutrition is a lifestyle optimization that has been shown to be of great importance in cancer initiation, progression, and metastasis. Dozens of clinical trials are currently in progress that focus on the nutritional modifications that cancer patients can make prior to and during medical care that increase the efficacy of treatment. In this review, we discuss various nutritional inventions for cancer patients and the analytical approaches to characterize the downstream molecular effects. We first begin by briefly explaining the many different forms of nutritional intervention currently being used in cancer treatment as well as their motivating biology. The forms of nutrient modulation described in this review include calorie restriction, the different practices of fasting, and carbohydrate restriction. The review then shifts to explain how proteomics is used to determine biomarkers of cancer and how it can be utilized in the future to determine the metabolic phenotype of a tumor, and inform physicians if nutritional intervention should be recommended for a cancer patient. Nutrigenomics aims to understand the relationship of nutrients and gene expression and can be used to understand the downstream molecular effects of nutrition restriction, partially through proteomic analysis. Proteomics is just beginning to be used as cancer diagnostic and predictive tools. However, these approaches have not been used to their full potential to understand nutritional intervention in cancer. Graphical abstract ᅟ.
Collapse
|