1
|
Segl M, Stutz H. Bottom-Up Analysis of Proteins by Peptide Mass Fingerprinting with tCITP-CZE-ESI-TOF MS After Tryptic Digest. Methods Mol Biol 2022; 2531:93-106. [PMID: 35941481 DOI: 10.1007/978-1-0716-2493-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of proteins in samples of moderate to complex composition is primarily done by bottom-up approaches. Therefore, proteins are enzymatically digested, mostly by trypsin, and the resulting peptides are then separated prior to their transfer to a mass spectrometer. The following protocol portrays a bottom-up method, which was optimized for the application of CZE-ESI-TOF MS. Protein denaturation is achieved by addition of 2,2,2-trifluoroethanol (TFE) and heat treatment. Afterwards, disulfide bonds are reduced with tris-(2-carboxyethyl)phosphine (TCEP) and subsequently alkylated with iodoacetamide (IAA). The tryptic digest is performed in an ammonium bicarbonate buffer at pH 8.0. The digested protein sample is then concentrated in-capillary by transient capillary isotachophoresis (tCITP) with subsequent CZE separation of tryptic peptides in an acidic background electrolyte. Hyphenation to a time-of-flight (TOF) mass spectrometer is carried out by a triple-tube coaxial sheath flow interface, which uses electrospray ionization (ESI). Peptide identification is done by peptide mass fingerprinting (PMF). The protocol is outlined exemplarily for a model protein, i.e., bovine β-lactoglobulin A.
Collapse
Affiliation(s)
- Marius Segl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria
| | - Hanno Stutz
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria.
- Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University of Salzburg, Salzburg, Austria.
| |
Collapse
|
2
|
Melzer T, Wimmer B, Bock S, Posch TN, Huhn C. Challenges and applications of isotachophoresis coupled to mass spectrometry: A review. Electrophoresis 2020; 41:1045-1059. [DOI: 10.1002/elps.201900454] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Tanja Melzer
- Institute of Physical and Theoretical ChemistryEberhard Karls Universität Tübingen Germany
| | - Benedikt Wimmer
- Institute of Physical and Theoretical ChemistryEberhard Karls Universität Tübingen Germany
| | - Stephanie Bock
- Institute of Physical and Theoretical ChemistryEberhard Karls Universität Tübingen Germany
| | | | - Carolin Huhn
- Institute of Physical and Theoretical ChemistryEberhard Karls Universität Tübingen Germany
| |
Collapse
|
3
|
Khnouf R, Han C. Isotachophoresis-Enhanced Immunoassays: Challenges and opportunities. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.2966028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
4
|
Wu H, Yi L, Wojcik R, Shi T, Tang K. A separation voltage polarity switching method for higher sample loading capacity and better separation resolution in transient capillary isotachophoresis separation. Analyst 2019; 144:454-462. [PMID: 30444223 DOI: 10.1039/c8an01779d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A separation voltage polarity switching transient capillary isotachophoresis (PS-tCITP) was developed to overcome a major sample loading volume limitation in transient capillary isotachophoresis (tCITP). The fundamental idea of PS-tCITP is to let sample ions move back and forth in a separation capillary during their initial isotachophoresis focusing stage by switching the polarity of the separation voltage, in order to both increase the sample loading volume and improve the separation efficiency as compared to the conventional tCITP method. The experimental evaluation of the novel PS-tCITP method by using two peptide standards at 2 μM concentration showed that the maximum sample loading volume could be increased from 45% of the total separation capillary volume in tCITP to 70% in PS-tCITP, which resulted in a more than 1.5 fold increase in the peptide peak intensity at a given length/volume of the separation capillary. Due to the consecutive focusing of sample volume from each polarity switching of the separation voltage, the separation time window at a given sample loading volume was also increased significantly in PS-tCITP as compared to tCITP. Experiment comparison between tCITP and PS-tCITP at 45% sample loading volume using the same setup showed that the migration time difference between the two peptide peaks increased from 0.3 min in tCITP to 0.363 min in PS-tCITP with similar peak widths and heights, resulting in roughly a 21% improvement in separation resolution. The performance advantages of PS-tCITP separation over tCITP separation were further verified by using a mixture of six peptide standards.
Collapse
Affiliation(s)
- Huanming Wu
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, P. R. China
| | | | | | | | | |
Collapse
|
5
|
Stock LG, Wildner S, Regl C, Gadermaier G, Huber CG, Stutz H. Monitoring of Deamidation and Lanthionine Formation in Recombinant Mugwort Allergen by Capillary Zone Electrophoresis (CZE)-UV and Transient Capillary Isotachophoresis-CZE-Electrospray Ionization-TOF-MS. Anal Chem 2018; 90:11933-11940. [PMID: 30179456 DOI: 10.1021/acs.analchem.8b02328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The response to thermal stress is an important parameter relevant for characterizing the biological activity and long-term stability of recombinant proteins, which may show irreversible, pH dependent structural changes under these conditions. We selected the recombinant pollen allergen of mugwort ( Artemisia vulgaris) rArt v 3.0201 as a relevant model to study structural changes due to thermal and pH stress by means of capillary zone electrophoresis (CZE)-UV and capillary zone electrophoresis (CZE)-electrospray ionization (ESI)-TOF-MS. Therefore, this recombinant protein was exposed to 95 °C under acidic (pH 3.4) and slightly alkaline (pH 7.3) conditions for up to 120 min. CZE-UV data showed a continuous degradation of the allergen accompanied by the gradual formation of several reaction products. Characterization of novel allergen variants occurring at longer migration times was done via CZE-ESI-TOF-MS using in-capillary transient capillary isotachophoresis (tCITP) preconcentration to facilitate the identification of minor variants. MS data revealed various modifications of rArt v 3.0201 in response to heating. Variants with deamidations and sulfur-related modifications including both yield and loss of sulfur were identified at increased migration times. Desulfurization produced allergen variants with up to four lanthionines that replaced initial disulfide bonds. In addition, mass spectra revealed shifts in the charge state distribution which indicate concomitant conformational alterations. Moreover, several low-abundant oxidized variants were identified. With extended thermal stress, the portfolio of variants increased and progressively shifted toward rArt v 3.0201 with high lanthionine content. The kinetics of conversion and the complexity of variant composition were pH dependent and increased under alkaline conditions.
Collapse
Affiliation(s)
- Lorenz G Stock
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| | - Sabrina Wildner
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| | - Christof Regl
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| | - Gabriele Gadermaier
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| | - Christian G Huber
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| | - Hanno Stutz
- Department of Biosciences , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria.,Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Hellbrunner Straße 34 , 5020 Salzburg , Austria
| |
Collapse
|
6
|
Quirino JP, Grochocki W, Markuszewski MJ. Sample Concentration of Charged Small Molecules and Peptides in Capillary Electrophoresis by Micelle to Cyclodextrin Stacking. Anal Chem 2017; 89:13422-13428. [DOI: 10.1021/acs.analchem.7b03700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Joselito P. Quirino
- Australian
Centre for Research on Separation Science (ACROSS), School of Physical
Sciences-Chemistry, University of Tasmania, Hobart 7001, Australia
| | - Wojciech Grochocki
- Australian
Centre for Research on Separation Science (ACROSS), School of Physical
Sciences-Chemistry, University of Tasmania, Hobart 7001, Australia
- Department
of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| | - Michał J. Markuszewski
- Department
of Biopharmaceutics and Pharmacodynamics, Medical University of Gdansk, Gdansk, Poland
| |
Collapse
|
7
|
Wang C, Lee CS, Smith RD, Tang K. Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification. Anal Chem 2013; 85:7308-15. [PMID: 23789856 PMCID: PMC3744340 DOI: 10.1021/ac401202c] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A novel sheathless capillary isotachophoresis (CITP/CZE)-mass spectrometry (MS) interface featuring a large inner diameter (i.d.) separation capillary, and a detachable small i.d. porous electrospray ionization (ESI) emitter was developed in this study to simultaneously achieve large sample loading capacity and stable nanoESI operation. Crucial operating parameters, including sample loading volume, flow rate, and separation window, were systematically investigated to attain optimum CITP/CZE separation efficiency and MS detection sensitivity. The performance of CITP/CZE-nanoESI-MS using the new sheathless interface was evaluated for its achievable low limit of quantification (LOQ) by analyzing targeted peptides, leu-enkephalin and angiotensin II, spiked in a BSA tryptic digest matrix at different concentrations. A linear dynamic range spanning 4.5 orders of magnitude and a 10 pM LOQ with measurement reproducibility of the CV < 22% were obtained experimentally for both targeted peptides, representing a 5-fold sensitivity improvement as compared to using the sheath liquid interface developed previously.1.
Collapse
Affiliation(s)
- Chenchen Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Cheng S. Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Keqi Tang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| |
Collapse
|
8
|
Wang C, Fang X, Lee CS. Recent advances in capillary electrophoresis-based proteomic techniques for biomarker discovery. Methods Mol Biol 2013; 984:1-12. [PMID: 23386332 DOI: 10.1007/978-1-62703-296-4_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Due to the inherent disadvantage of biomarker dilution in complex biological fluids such as serum/plasma, urine, and saliva, investigative studies directed at tissues obtained from the primary site of pathology probably afford the best opportunity for the discovery of disease biomarkers. Still, the large variation of protein relative abundances with clinical specimens often exceeds the dynamic range of currently available proteomic techniques. Furthermore, since the sizes of human tissue biopsies are becoming significantly smaller due to the advent of minimally invasive methods and early detection and treatment of lesions, a more effective discovery-based proteomic technology is critically needed to enable comprehensive and comparative studies of protein profiles that will have diagnostic and therapeutic relevance.This review therefore focuses on the most recent advances in capillary electrophoresis-based single and multidimensional separations coupled with mass spectrometry for performing comprehensive proteomic analysis of clinical specimens. In addition to protein identification, monitoring quantitative changes in protein expression is essential for the discovery of disease-associated biomarkers. Comparative proteomics involving measurements in changes of biological pathways or functional processes are further expected to provide relevant markers and networks, molecular relationships among different stages of disease, and molecular mechanisms that drive the progression of disease.
Collapse
Affiliation(s)
- Chenchen Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | | |
Collapse
|
9
|
Wang C, Lee CS, Smith RD, Tang K. Ultrasensitive sample quantitation via selected reaction monitoring using CITP/CZE-ESI-triple quadrupole MS. Anal Chem 2012; 84:10395-403. [PMID: 23140208 DOI: 10.1021/ac302616m] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate the direct coupling of transient capillary isotachophoresis/capillary zone electrophoresis (CITP/CZE) with a high-sensitivity triple quadrupole mass spectrometer operating in selected reaction monitoring (SRM) mode for sample quantitation. The capability of CITP/CZE for in situ sample enrichment and separation has been shown to significantly improve the analytical figures of merit. A linear dynamic range spanning 4 orders of magnitude was observed. An average signal-to-noise ratio (S/N) of 49.6 was observed for 50 amol of targeted peptide in the presence of a complex and much more abundant bovine serum albumin (BSA) digest. Correlation of variation (CV) of <10% for peak area was measured from triplicate sample analyses at 50 pM peptide concentration, showing good reproducibility of this online CITP/CZE-SRM mass spectrometry (MS) platform, and with limit of quantitation (LOQ) demonstrated to be well below 50 pM.
Collapse
Affiliation(s)
- Chenchen Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, 20742, United States
| | | | | | | |
Collapse
|
10
|
Fang X, Wang C, Balgley BM, Zhao K, Wang W, He F, Weil RJ, Lee CS. Targeted tissue proteomic analysis of human astrocytomas. J Proteome Res 2012; 11:3937-46. [PMID: 22794670 DOI: 10.1021/pr300303t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not only serves as a synergistic strategy to characterize low abundance proteins, but it can also be employed to conduct comparative proteomic studies of human astrocytomas. A set of fresh frozen brain biopsies were selectively microdissected to provide an enriched, high quality, and reproducible sample of tumor cells. Despite sharing many common proteins, there are significant differences in the protein expression level among different grades of astrocytomas. A large number of proteins, such as plasma membrane proteins EGFR and Erbb2, are up-regulated in glioblastoma. Besides facilitating the prioritization of follow-on biomarker selection and validation, comparative proteomics involving measurements in changes of pathways are expected to reveal the molecular relationships among different pathological grades of gliomas and potential molecular mechanisms that drive gliomagenesis.
Collapse
Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Dawod M, Chung DS. High-sensitivity capillary and microchip electrophoresis using electrokinetic supercharging. J Sep Sci 2011; 34:2790-9. [DOI: 10.1002/jssc.201100384] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/01/2011] [Accepted: 06/01/2011] [Indexed: 12/22/2022]
|
12
|
Fonslow BR, Carvalho PC, Academia K, Freeby S, Xu T, Nakorchevsky A, Paulus A, Yates JR. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT. J Proteome Res 2011; 10:3690-700. [PMID: 21702434 DOI: 10.1021/pr200304u] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ideally, shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundance peptides and (2) enrichment of low abundance proteins increased the probability of sampling their corresponding more abundant peptides. Both mechanisms also contributed to dramatic increases in the quantity of peptides identified and the quality of MS/MS spectra acquired due to increases in precursor intensity of peptides from low abundance proteins. From our large data set of identified proteins, we categorized the dominant physicochemical factors that facilitate proteome equalization with a hexapeptide library. These results illustrate that equalization of the dynamic range of the cellular proteome is a promising methodology to improve low abundance protein identification confidence, reproducibility, and sequence coverage in shotgun proteomics experiments, opening a new avenue of research for improving proteome coverage.
Collapse
Affiliation(s)
- Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Arribas AS, Moreno M, Bermejo E, Zapardiel A, Chicharro M. CZE separation of amitrol and triazine herbicides in environmental water samples with acid-assisted on-column preconcentration. Electrophoresis 2010; 32:275-83. [DOI: 10.1002/elps.201000371] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/22/2010] [Accepted: 10/14/2010] [Indexed: 11/08/2022]
|
14
|
Fang X, Balgley BM, Wang W, Park DM, Lee CS. Comparison of multidimensional shotgun technologies targeting tissue proteomics. Electrophoresis 2010; 30:4063-70. [PMID: 19960471 DOI: 10.1002/elps.200900367] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A compelling need exists for the development of technologies that facilitate and accelerate the discovery of novel protein biomarkers with therapeutic and diagnostic potential. Comparisons among shotgun proteome technologies, including capillary isotachophoresis (CITP)-based multidimensional separations and multidimensional LC system, are therefore performed in this study regarding their abilities to address the challenges of protein complexity and relative abundance inherent in glioblastoma multiforme-derived cancer stem cells. Comparisons are conducted using a single processed protein digest with equal sample loading, identical second-dimension separation (RPLC) and MS conditions, and consistent search parameters and cutoff established by the target-decoy determined false-discovery rate. Besides achieving superior overall proteome performance in total peptide, distinct peptide, and distinct protein identifications; analytical reproducibility of the CITP proteome platform coupled with the spectral counting approach are determined by a Pearson R(2) value of 0.98 and a CV of 15% across all proteins quantified. In contrast, extensive fraction overlapping in strong cation exchange greatly limits the ability of multidimensional LC separations for mining deeper into the tissue proteome as evidenced by the poor coverage in various protein functional categories and key protein pathways. The CITP proteomic technology, equipped with selective analyte enrichment and ultrahigh resolving power, is expected to serve as a critical component in the overall toolset required for biomarker discovery via shotgun proteomic analysis of tissue specimens.
Collapse
Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | | | | | | | |
Collapse
|
15
|
Fang X, Balgley BM, Lee CS. Recent advances in capillary electrophoresis-based proteomic techniques for biomarker discovery. Electrophoresis 2010; 30:3998-4007. [PMID: 19960464 DOI: 10.1002/elps.200900219] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A compelling need exists for the development of technologies that facilitate and accelerate the discovery of novel protein biomarkers with therapeutic and diagnostic potential. The inherent disadvantage of biomarker dilution in complex biological fluids such as serum/plasma, urine, and saliva necessitates highly sensitive analytical approaches, often exceeding the dynamic range of currently available proteomic platforms. Thus, investigative studies directed at tissues obtained from the primary site of pathology probably afford the best opportunity for the discovery of disease biomarkers. This review therefore focuses on the most recent advances in capillary electrophoresis-based single and multidimensional separations coupled with ESI-MS for performing comprehensive and comparative analysis of protein expression profiles within clinical specimens. Advanced sample preparation techniques, including tissue microdissection, detergent-based membrane protein extraction, and heat-induced protein retrieval, further enable targeted protein profiling of both fresh-frozen, formalin-fixed, and paraffin-embedded tissues. Comparative proteomics involving measurements in changes of biological pathways or functional processes are expected to provide relevant disease-associated markers and networks, molecular relationships among different stages of disease, and molecular mechanisms that drive the progression of disease. From a practical perspective, the evaluation of comparative proteomic dataset within a biological context is essential for high-throughput data validation, prioritization of follow-on biomarker selection, and validation experiments.
Collapse
Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | | | |
Collapse
|
16
|
Tran NT, Ayed I, Pallandre A, Taverna M. Recent innovations in protein separation on microchips by electrophoretic methods: An update. Electrophoresis 2010; 31:147-73. [DOI: 10.1002/elps.200900465] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
17
|
In-line preconcentration of oxidized and reduced glutathione in capillary zone electrophoresis using transient isotachophoresis under strong counter-electroosmotic flow. J Chromatogr A 2009; 1216:8665-70. [DOI: 10.1016/j.chroma.2009.10.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 10/06/2009] [Accepted: 10/09/2009] [Indexed: 11/20/2022]
|
18
|
Abstract
Sample stacking techniques remain an important tool for enhancement of the selectivity and sensitivity of analyses in contemporary CZE. This contribution reviews new knowledge on this topic published since 2006. It is organized according to the operational principles used, which include concentration adjustment, application of a pH step, MEKC and sweeping, and transient ITP. Techniques combining several of these principles and comparative studies are also included.
Collapse
Affiliation(s)
- Zdena Malá
- Institute of Analytical Chemistry of the ASCR, Brno, Czech Republic
| | | | | | | |
Collapse
|
19
|
Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
|
20
|
Chen Y, Zhang L, Xu L, Lin JM, Chen G. Assay of bradykinin metabolites in human body fluids by CE-LIF coupled with transient ITP preconcentration. Electrophoresis 2009; 30:2300-6. [DOI: 10.1002/elps.200800477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
21
|
Lagarrigue M, Bossée A, Bégos A, Delaunay N, Varenne A, Gareil P, Bellier B. Analysis of nerve agent degradation products in high-conductivity matrices by transient ITP preconcentration and CZE separation coupled to ESI-MS. Electrophoresis 2009; 30:1522-30. [DOI: 10.1002/elps.200800438] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
22
|
Abstract
In the postgenomic era, proteomics has become a dominant field for identifying and quantifying the complex protein machinery of the cell. The expression levels, posttranslational modifications, and specific interactions of proteins control the biology of such processes as development, differentiation, and signal transduction. Studies of the proteins involved in these processes often lead to a better understanding of biology and of human disease. Powerful separation techniques and sensitive detection methods enable researchers to untangle these complicated networks of processes. CE coupled with either MS or LIF are two of the techniques that make this possible. This review will cover proven CE-based methods for proteomics on the cell and tissue level and their application in biological and clinical studies, relevant new developments in enabling technology such as microfluidic CE-MS demonstrated on model systems, and comment on the future of CE in proteomics.
Collapse
MESH Headings
- Amino Acid Sequence
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Humans
- Molecular Sequence Data
- Proteins/analysis
- Proteins/genetics
- Proteome/analysis
- Proteomics/methods
- Sequence Alignment
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Collapse
Affiliation(s)
- Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | |
Collapse
|
23
|
Chapter 3 Proteome Characterization of Mouse Brain Mitochondria Using Electrospray Ionization Tandem Mass Spectrometry. Methods Enzymol 2009; 457:49-62. [DOI: 10.1016/s0076-6879(09)05003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
24
|
High-sensitivity capillary and microchip electrophoresis using electrokinetic supercharging preconcentration. J Chromatogr A 2009; 1216:660-70. [DOI: 10.1016/j.chroma.2008.10.077] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/02/2008] [Accepted: 10/07/2008] [Indexed: 11/24/2022]
|
25
|
Pantůčková P, Gebauer P, Boček P, Křivánková L. Electrolyte systems for on-line CE-MS: Detection requirements and separation possibilities. Electrophoresis 2009; 30:203-14. [DOI: 10.1002/elps.200800262] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
26
|
Breadmore MC, Thabano JRE, Dawod M, Kazarian AA, Quirino JP, Guijt RM. Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2006-2008). Electrophoresis 2009; 30:230-48. [DOI: 10.1002/elps.200800435] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
27
|
Recent applications of capillary electrophoresis–mass spectrometry (CE–MS): CE performing functions beyond separation. Anal Chim Acta 2008; 627:3-24. [DOI: 10.1016/j.aca.2008.04.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Revised: 04/02/2008] [Accepted: 04/08/2008] [Indexed: 11/18/2022]
|
28
|
Fang X, Wang W, Yang L, Chandrasekaran K, Kristian T, Balgley BM, Lee CS. Application of capillary isotachophoresis-based multidimensional separations coupled with electrospray ionization-tandem mass spectrometry for characterization of mouse brain mitochondrial proteome. Electrophoresis 2008; 29:2215-23. [PMID: 18425750 DOI: 10.1002/elps.200700609] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
By employing a capillary ITP (CITP)/CZE-based proteomic technology, a total of 1795 distinct mouse Swiss-Prot protein entries (or 1705 nonredundant proteins) are identified from synaptic mitochondria isolated from mouse brain. The ultrahigh resolving power of CITP/CZE is evidenced by the large number of distinct peptide identifications measured from each CITP fraction together with the low peptide fraction overlapping among identified peptides. The degree of peptide overlapping among CITP fractions is even lower than that achieved using combined CIEF/nano-RP LC separations for the analysis of the same mitochondrial sample. When evaluating the protein sequence coverage by the number of distinct peptides mapping to each mitochondrial protein identification, CITP/CZE similarly achieves superior performance with 1041 proteins (58%) having 3 or more distinct peptides, 233 (13%) having 2 distinct peptides, and 521 (29%) having a single distinct peptide. The reproducibility of protein identifications is found to be around 86% by comparing proteins identified from repeated runs of the same mitochondrial sample. The analysis of the mouse mitochondrial proteome by two CITP/CZE runs results in the detection of 2095 distinct mouse Swiss-Prot protein entries (or 1992 nonredundant proteins), corresponding to 59% coverage of the updated Maestro mitochondrial reference set. The collective analysis from combined CITP/CZE and CIEF-based proteomic studies yields the identification of 2191 distinct mitochondrial protein entries (or 2082 nonredundant proteins), corresponding to 76% coverage of the MitoP2-database reference set.
Collapse
Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | | | | | | | | | | | |
Collapse
|
29
|
Tomás R, Klepárník K, Foret F. Multidimensional liquid phase separations for mass spectrometry. J Sep Sci 2008; 31:1964-79. [PMID: 18615817 DOI: 10.1002/jssc.200800113] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Large part of the current research in biology, medicine, and biotechnology depends on the analysis of DNA (genomics), proteins (proteomics), or metabolites (metabolomics). The advances in biotechnology also command development of adequate analytical instrumentation capable to analyze minute amounts of samples. The analysis of the content of single cells may serve as an example of ultimate analytical applications. Most of the separation techniques have been developed in the last three decades and alternative approaches are being investigated. At present, the main protocols for analyses of complex mixtures include 2-DE (IEF) followed by electrophoresis in SDS polyacrylamide gel (SDS-PAGE) and chromatographic techniques. Information-rich techniques such as MS and NMR are essential for the identification and structure analysis of the analyzed compounds. High resolution separation of the individual sample components is often a prerequisite for success. High resolution proteomic analysis in the majority of laboratories still relies on the time consuming and laborious offline methods. This review highlights some of the important aspects of 2-D separations including microfluidics.
Collapse
Affiliation(s)
- Roman Tomás
- Institute of Analytical Chemistry, Brno, Czech Republic
| | | | | |
Collapse
|
30
|
Kostal V, Katzenmeyer J, Arriaga EA. Capillary electrophoresis in bioanalysis. Anal Chem 2008; 80:4533-50. [PMID: 18484738 DOI: 10.1021/ac8007384] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vratislav Kostal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | | | | |
Collapse
|
31
|
Balgley BM, Wang W, Fang X, DeVoe DL, Lee CS. Capillary Electrophoretic Separations for Clinical Proteomics. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
32
|
Busnel JM, Lion N, Girault HH. Electrokinetic supercharging for highly efficient peptide preconcentration in capillary zone electrophoresis. Electrophoresis 2008; 29:1565-72. [DOI: 10.1002/elps.200700643] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
33
|
Westman-Brinkmalm A, Silberring J, Brinkmalm G. Separation Methods. Mass Spectrom (Tokyo) 2008. [DOI: 10.1002/9780470395813.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
34
|
Lin CC, Hsu BK, Chen SH. Integrated isotachophoretic stacking and gel electrophoresis on a plastic substrate and variations in detection dynamic range. Electrophoresis 2008; 29:1228-36. [DOI: 10.1002/elps.200700479] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
35
|
Simpson SL, Quirino JP, Terabe S. On-line sample preconcentration in capillary electrophoresis. J Chromatogr A 2008; 1184:504-41. [DOI: 10.1016/j.chroma.2007.11.001] [Citation(s) in RCA: 269] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 10/30/2007] [Accepted: 11/01/2007] [Indexed: 02/06/2023]
|
36
|
Macià A, Borrull F, Calull M, Benavente F, Hernández E, Sanz-Nebot V, Barbosa J, Aguilar C. Sensitivity enhancement for the analysis of naproxen in tap water by solid-phase extraction coupled in-line to capillary electrophoresis. J Sep Sci 2008; 31:872-80. [DOI: 10.1002/jssc.200700593] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
37
|
Xu H, Yang L, Wang W, Shi SR, Liu C, Liu Y, Fang X, Taylor CR, Lee CS, Balgley BM. Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 2008; 7:1098-108. [PMID: 18257518 DOI: 10.1021/pr7006768] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Formalin-fixed and paraffin-embedded tissues represent the vast majority of archived tissue. Access to such tissue specimens via shotgun-based proteomic analyses may open new avenues for both prospective and retrospective translational research. In this study, we evaluate the effects of fixation time on antigen retrieval for the purposes of shotgun proteomics. For the first time, we demonstrate the capability of a capillary isotachophoresis (CITP)-based proteomic platform for the shotgun proteomic analysis of proteins recovered from FFPE tissues. In comparison to our previous studies utilizing capillary isoelectric focusing, the CITP-based analysis is more robust and increases proteome coverage. In this case, results from three FFPE liver tissues yield a total of 4098 distinct Swiss-Prot identifications at a 1% false-discovery rate. To judge the accuracy of these assignments, immunohistochemistry is performed on a panel of 17 commonly assayed proteins. These proteins span a wide range of protein abundances as inferred from relative quantitation via spectral counting. Among the panel were 4 proteins identified by a single peptide hit, including three clusters of differentiation (CD) markers: CD74, CD117, and CD45. Because single peptide hits are often regarded with skepticism, it is notable that all proteins tested by IHC stained positive.
Collapse
Affiliation(s)
- Haifeng Xu
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, Maryland 20878, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Gaspar A, Englmann M, Fekete A, Harir M, Schmitt-Kopplin P. Trends in CE-MS 2005–2006. Electrophoresis 2008; 29:66-79. [DOI: 10.1002/elps.200700721] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
39
|
Abstract
The article brings a comprehensive survey of recent developments and applications of high-performance capillary electromigration methods, zone electrophoresis, ITP, IEF, affinity electrophoresis, EKC, and electrochromatography, to analysis, preparation, and physicochemical characterization of peptides. New approaches to the theoretical description and experimental verification of electromigration behavior of peptides and to methodology of their separations, such as sample preparation, adsorption suppression, and detection, are presented. Novel developments in individual CE and CEC modes are shown and several types of their applications to peptide analysis are presented: conventional qualitative and quantitative analysis, purity control, determination in biomatrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid and sequence analysis, and peptide mapping of proteins. Some examples of micropreparative peptide separations are given and capabilities of CE and CEC techniques to provide important physicochemical characteristics of peptides are demonstrated.
Collapse
Affiliation(s)
- Václav Kasicka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| |
Collapse
|
40
|
|
41
|
Yang X, Yuan H, Wang C, Zhao S, Xiao D, Choi MMF. In-column fiber-optic laser-induced fluorescence detection for CE. Electrophoresis 2007; 28:3105-14. [PMID: 17674418 DOI: 10.1002/elps.200600815] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A highly sensitive in-column fiber-optic LIF detector for CE has been constructed and evaluated. In this detection system, a 457-nm diode-pumped solid-state blue laser was used as the excitation light source and an optical fiber (40 mum od) was used to transmit the excitation light. One end of the optical fiber was inserted into the separation capillary and was in situ positioned at the detection window. The other end of the fiber was protruded from the capillary to capture the excitation light beam from the blue laser. Fluorescence emission was collected by a 40 x microscope objective, focused on a spatial filter, and passed through a yellow color filter before reaching the photomultiplier tube. The present CE-fluorescence detection is a simple and compact optical system. It reduces the laser scattering effect from the capillary and fiber as compared to the conventional LIF detection for CE. Its utility was successfully demonstrated by the separation and determination of D-penicillamine labeled with naphthalene-2,3-dicarboxaldehyde. The detection limit was 0.8 nM (S/N = 3). The present detection scheme has been proven to be attractive for sensitive fluorescence detection for CE.
Collapse
Affiliation(s)
- Xiupei Yang
- College of Chemistry, Sichuan University, Chengdu, PR China
| | | | | | | | | | | |
Collapse
|
42
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:689-700. [PMID: 17474104 DOI: 10.1002/jms.1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
|