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Lazar IM. Achieving Stable Electrospray Ionization Mass Spectrometry Detection from Microfluidic Chips. Methods Mol Biol 2019; 1906:225-237. [PMID: 30488396 DOI: 10.1007/978-1-4939-8964-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The past two decades have witnessed remarkable advances in the development of microfluidic devices as bioanalytical platforms for the analysis of biological molecules. The implementation of mass spectrometry (MS) detection systems on these devices has become inevitable, and various chip-MS ionization interfaces have been developed. As electrospray ionization (ESI) is particularly relevant for the analysis of large biological molecules such as proteins or peptides, efforts have focused on advancing interfaces that meet the demands of nano-separation techniques that are typically used prior to MS detection. Achieving stable ESI conditions that enable sensitive MS detection is, however, not trivial, especially when the spray is generated from a microfabricated platform. This chapter is aimed at providing a step-by-step protocol for producing stable and efficient electrospray sample ionization from microfluidic chips that are used for capillary electrophoresis (CE) separations.
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Affiliation(s)
- Iulia M Lazar
- Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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Deng J, Julian MH, Lazar IM. Partial enzymatic reactions: A missed opportunity in proteomics research. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2065-2073. [PMID: 30221418 PMCID: PMC6636927 DOI: 10.1002/rcm.8283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 05/05/2023]
Abstract
RATIONALE Biological studies are conducted at ever-increasing rates by relying on proteomic workflows. Although data acquisition by mass spectrometry is highly automated and rapid, sample preparation continues to be the bottleneck of developing high-throughput workflows. Enzymatic protein processing, in particular, involves time-consuming protocols that can extend from one day to another. To address this gap, we developed and evaluated simple, in-solution tryptic enzymatic reactions that unfold within a few minutes, and demonstrate the utility of the methodology for the rapid analysis of proteins originating from cancer cell extracts. METHODS Tryptic enzymatic reactions were conducted for 7-60 min, and the results were compared with that of a routine approach conducted for 18 h. No other reaction conditions were changed relative to the 18 h procedure. The reaction products were analyzed by nanospray high-performance liquid chromatography/tandem mass spectrometry (nano-HPLC/MS/MS), and the quality of the products was assessed in terms of peptide/protein identifications, sequence coverage, peptide length, missed-cleavage sites, quality of generated ions, and peptide hydrophilic/hydrophobic properties. RESULTS The results demonstrate that brief, and therefore incomplete, enzymatic processes lead to a large number of peptide fragments that improve protein sequence and proteome coverage, that the tandem mass spectra produced from these peptides are of high quality for reliable protein identifications, and that the physical properties of peptides are prone to supporting the development of alternative multi-dimensional separations and middle-down proteomics analysis strategies. The reproducibility of generating the same peptides within a few minutes of enzymatic digestion was remarkably close to that obtained from 18 h long reactions, and the combined results of short and long reactions increased proteome coverage by ~40%. CONCLUSIONS We demonstrate that partial enzymatic reactions conducted on short time-scales represent a valuable asset to proteomic studies, and propose their implementation either as simple, cost-effective, stand-alone protocols for substantially streamlining the analysis of biological samples, or as complementary protocols, for improving protein sequence and proteome coverage.
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Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061, USA
| | - Morgan H. Julian
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061, USA
| | - Iulia M. Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA 24061, USA
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Deng J, Ikenishi F, Smith N, Lazar IM. Streamlined microfluidic analysis of phosphopeptides using stable isotope-labeled synthetic peptides and MRM-MS detection. Electrophoresis 2018; 39:3171-3184. [PMID: 30216485 DOI: 10.1002/elps.201800133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/07/2022]
Abstract
Modern high-throughput and high-content biological research is performed with advanced instrumentation and complex and time-consuming protocols, which, as a whole, pose a challenge for routine implementation in a research laboratory. In support of a "bioanalytical toolbox" with potential utility for exploring cellular functions mediated via protein phosphorylation-a post-translational modification (PTM) with essential regulatory roles in a variety of cellular processes-in this work, we describe the development of a simple, integrated microfluidic chip that can perform targeted, quantitative analysis of phosphopeptides involved in cancer-relevant signaling pathways. The microfluidic device comprises microreactors packed with C18 and TiO2 particles for on-chip solid phase extraction (SPE) and phosphopeptide enrichment, and an ESI interface for facilitating multiple reaction monitoring (MRM)-mass spectrometry (MS) detection. The chips are demonstrated for the detection of three phosphopeptides involved in ERBB2/MAPK signaling pathways, selected from the outcome of a proteomic study involving EGF stimulation of SKBR3/HER2+ breast cancer cells. The data demonstrate that the proposed microfluidic strategy can be used for the MS quantification of phosphopeptides in the low nM range from cell lysates without any prior sample pretreatment, fractionation or bioaffinity enrichment, and is generally applicable to the analysis of any phosphopeptide targets.
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Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Fumio Ikenishi
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Nicole Smith
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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Lazar IM, Deng J, Smith N. Fast Enzymatic Processing of Proteins for MS Detection with a Flow-through Microreactor. J Vis Exp 2016:e53564. [PMID: 27078683 DOI: 10.3791/53564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The vast majority of mass spectrometry (MS)-based protein analysis methods involve an enzymatic digestion step prior to detection, typically with trypsin. This step is necessary for the generation of small molecular weight peptides, generally with MW < 3,000-4,000 Da, that fall within the effective scan range of mass spectrometry instrumentation. Conventional protocols involve O/N enzymatic digestion at 37 ºC. Recent advances have led to the development of a variety of strategies, typically involving the use of a microreactor with immobilized enzymes or of a range of complementary physical processes that reduce the time necessary for proteolytic digestion to a few minutes (e.g., microwave or high-pressure). In this work, we describe a simple and cost-effective approach that can be implemented in any laboratory for achieving fast enzymatic digestion of a protein. The protein (or protein mixture) is adsorbed on C18-bonded reversed-phase high performance liquid chromatography (HPLC) silica particles preloaded in a capillary column, and trypsin in aqueous buffer is infused over the particles for a short period of time. To enable on-line MS detection, the tryptic peptides are eluted with a solvent system with increased organic content directly in the MS ion source. This approach avoids the use of high-priced immobilized enzyme particles and does not necessitate any aid for completing the process. Protein digestion and complete sample analysis can be accomplished in less than ~3 min and ~30 min, respectively.
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Deng J, Lazar IM. Proteolytic Digestion and TiO2 Phosphopeptide Enrichment Microreactor for Fast MS Identification of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:686-698. [PMID: 26883530 DOI: 10.1007/s13361-015-1332-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/20/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
The characterization of phosphorylation state(s) of a protein is best accomplished by using isolated or enriched phosphoprotein samples or their corresponding phosphopeptides. The process is typically time-consuming as, often, a combination of analytical approaches must be used. To facilitate throughput in the study of phosphoproteins, a microreactor that enables a novel strategy for performing fast proteolytic digestion and selective phosphopeptide enrichment was developed. The microreactor was fabricated using 100 μm i.d. fused-silica capillaries packed with 1-2 mm beds of C18 and/or TiO2 particles. Proteolytic digestion-only, phosphopeptide enrichment-only, and sequential proteolytic digestion/phosphopeptide enrichment microreactors were developed and tested with standard protein mixtures. The protein samples were adsorbed on the C18 particles, quickly digested with a proteolytic enzyme infused over the adsorbed proteins, and further eluted onto the TiO2 microreactor for enrichment in phosphopeptides. A number of parameters were optimized to speed up the digestion and enrichments processes, including microreactor dimensions, sample concentrations, digestion time, flow rates, buffer compositions, and pH. The effective time for the steps of proteolytic digestion and enrichment was less than 5 min. For simple samples, such as standard protein mixtures, this approach provided equivalent or better results than conventional bench-top methods, in terms of both enzymatic digestion and selectivity. Analysis times and reagent costs were reduced ~10- to 15-fold. Preliminary analysis of cell extracts and recombinant proteins indicated the feasibility of integration of these microreactors in more advanced workflows amenable for handling real-world biological samples. Graphical Abstract ᅟ.
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Affiliation(s)
- Jingren Deng
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
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Kohler I, Schappler J, Rudaz S. Highly sensitive capillary electrophoresis-mass spectrometry for rapid screening and accurate quantitation of drugs of abuse in urine. Anal Chim Acta 2013; 780:101-9. [DOI: 10.1016/j.aca.2013.03.065] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/27/2013] [Accepted: 03/31/2013] [Indexed: 10/26/2022]
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Cui H, Hua L, Hou K, Wu J, Chen P, Xie Y, Wang W, Li J, Li H. Coupling of stir bar sorptive extraction with single photon ionization mass spectrometry for determination of volatile organic compounds in water. Analyst 2012; 137:513-8. [DOI: 10.1039/c1an15876g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Catai JR, Toraño JS, de Jong GJ, Somsen GW. Efficient and highly reproducible capillary electrophoresis-mass spectrometry of peptides using Polybrene-poly(vinyl sulfonate)-coated capillaries. Electrophoresis 2006; 27:2091-9. [PMID: 16736451 DOI: 10.1002/elps.200500915] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The potential of capillaries noncovalently coated with a bilayer of oppositely charged polymers for the analysis of peptides by CE-MS was investigated. Bilayer coatings were produced by subsequently rinsing fused-silica capillaries with a solution of Polybrene (PB) and poly(vinyl sulfonate) (PVS). The PB-PVS coating showed to be fully compatible with MS detection causing no ionization suppression or background signals. The bilayer coating provided a considerable EOF at low pH, thereby facilitating the fast separation of peptides using a BGE of formic acid (pH 2.5). Under optimized CE-MS conditions, for enkephalin peptides high separation efficiencies were obtained with plate numbers in the range of 300,000-500,000. It is demonstrated that both the cancellation of the hydrodynamic capillary flow induced by the nebulizer gas and a sufficiently high-data acquisition rate are crucial for achieving these efficiencies. The overall performance of the CE-MS system using PB-PVS-coated capillaries was evaluated by the analysis of a tryptic digest of cytochrome c. The system provided an efficient separation of the peptide mixture, which could be effectively monitored by MS/MS detection allowing identification of at least 13 peptides within a time interval of 1.5 min. In addition, the PB-PVS coating proved to be very consistent yielding stable CE-MS patterns with highly favorable migration time reproducibilities (RSDs < 1% over a 3-day period).
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Affiliation(s)
- Jonatan R Catai
- Department of Biomedical Analysis, Utrecht University, The Netherlands
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Balcerzak M. An overview of analytical applications of time of flight-mass spectrometric (TOF-MS) analyzers and an inductively coupled plasma-TOF-MS technique. ANAL SCI 2003; 19:979-89. [PMID: 12880079 DOI: 10.2116/analsci.19.979] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A brief overview of the applications of time-of-flight mass spectrometry (TOF-MS) for analytical purposes is presented. The performance of TOF-MS combined with an inductively coupled plasma (ICP) ion source is discussed in detail. The advantages of TOF-MS detectors over the quadrupole mass filters for multi-elemental analysis of fast transient signals are discussed. The applications of ICP-TOF-MS for the detection of signals from laser ablation, electrothermal vaporization, gas and liquid chromatography, capillary electrophoresis and flow-injection analysis are reviewed.
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Affiliation(s)
- Maria Balcerzak
- Department of Analytical Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
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FURUMOTO T, FUKUMOTO T, WATARAI H. Capillary electrophoresis of nucleobases and nucleosides detected by TOF/MS. BUNSEKI KAGAKU 2003. [DOI: 10.2116/bunsekikagaku.52.1203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Tadao FURUMOTO
- Department of Chemistry, Graduate School of Science, Osaka University
| | - Takao FUKUMOTO
- Department of Chemistry, Graduate School of Science, Osaka University
| | - Hitoshi WATARAI
- Department of Chemistry, Graduate School of Science, Osaka University
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Lazar IM, Ramsey RS, Jacobson SC, Foote RS, Ramsey JM. Novel microfabricated device for electrokinetically induced pressure flow and electrospray ionization mass spectrometry. J Chromatogr A 2000; 892:195-201. [PMID: 11045489 DOI: 10.1016/s0021-9673(00)00335-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel microchip device for electrospray ionization has been fabricated and interfaced to a time-of-flight mass spectrometer. Fluid is electrokinetically transported through the chip to a fine fused-silica capillary inserted directly into a channel at the edge of the device. Electrospray is established at the tip of the capillary, which assures a stable, efficient spray. The electric potential necessary for electrospray generation and the voltage drop for electroosmotic pumping are supplied through an electrically permeable glass membrane contacting the fluidic channel holding the capillary. The membrane is fabricated on the microchip using standard photolithographic and wet chemical etching techniques. Performance relative to other microchip electrospray sources has been evaluated and the device tested for potential use as a platform for on-line electrophoretic detection. Sensitivity was found to be approximately three orders of magnitude better than spraying from the flat edge of the chip. The effect of the capillary on electroosmotic flow was examined both experimentally and theoretically.
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Affiliation(s)
- I M Lazar
- Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, TN 37831-6365, USA
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Abstract
The most demanding problems in proteomics continue to challenge modern mass spectrometry. Recent developments in instrument design have led to lower limits of detection, while new ion activation techniques and improved understanding of gas-phase ion chemistry have enhanced the capabilities of tandem mass spectrometry for peptide and protein structure elucidation. Future developments must address the., understanding of protein-protein interactions and the characterisation of the dynamic proteome.
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Affiliation(s)
- M J Chalmers
- Michael Barber Centre for Mass Spectrometry, Department of Chemistry, UMIST, Manchester, UK
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Collins DC, Tang Q, Wu N, Lee ML. Fast liquid chromatography/time-of-flight mass spectrometry using sol-gel bonded continuous-bed capillary columns. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/1520-667x(2000)12:8<442::aid-mcs2>3.0.co;2-q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wu N, Collins DC, Lippert JA, Xiang Y, Lee ML. Ultrahigh pressure liquid chromatography/time-of-flight mass spectrometry for fast separations. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/1520-667x(2000)12:8<462::aid-mcs5>3.0.co;2-f] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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