1
|
Reyes AJF, Kitata RB, Dela Rosa MAC, Wang YT, Lin PY, Yang PC, Friedler A, Yitzchaik S, Chen YJ. Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level. Anal Chim Acta 2021; 1155:338341. [PMID: 33766317 DOI: 10.1016/j.aca.2021.338341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/25/2022]
Abstract
Dysregulation of phosphorylation-mediated signaling drives the initiation and progression of many diseases. A substrate-specific kinase assay capable of quantifying the altered site-specific phosphorylation of its phenotype-dependent substrates provides better specificity to monitor a disease state. We report a sensitive and rapid substrate-specific kinase assay by integrating site-specific peptide reporter and multiple reaction monitoring (MRM)-MS platform for relative and absolute quantification of substrate-specific kinase activity at the sensitivity of nanomolar kinase and nanogram cell lysate. Using non-small cell lung cancer as a proof-of-concept, three substrate peptides selected from constitutive phosphorylation in tumors (HDGF-S165, RALY-S135, and NRD1-S94) were designed to demonstrate the feasibility. The assay showed good accuracy (<15% nominal deviation) and reproducibility (<15% CV). In PC9 cells, the measured activity for HDGF-S165 was 3.2 ± 0.2 fmol μg-1 min-1, while RALY-S135 and NRD1-S94 showed 4- and 20-fold higher activity at the sensitivity of 25 ng and 5 ng lysate, respectively, suggesting different endogenous kinases for each substrate peptide. Without the conventional shotgun phosphoproteomics workflow, the overall pipeline from cell lysate to MS data acquisition only takes 3 h. The multiplexed analysis revealed differences in the phenotype-dependent substrate phosphorylation profiles across six NSCLC cell lines and suggested a potential association of HDGF-S165 and NRD1-S94 with TKI resistance. With the ease of design, sensitivity, accuracy, and reproducibility, this approach may offer rapid and sensitive assays for targeted quantification of the multiplexed substrate-specific kinase activity of small amounts of sample.
Collapse
Affiliation(s)
- Aaron James F Reyes
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Mira Anne C Dela Rosa
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Yu-Ju Chen
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
| |
Collapse
|
2
|
Gode D, Schmitt C, Engel M, Volmer DA. Screening Dyrk1A inhibitors by MALDI-QqQ mass spectrometry: systematic comparison to established radiometric, luminescence, and LC-UV-MS assays. Anal Bioanal Chem 2014; 406:2841-52. [PMID: 24618988 DOI: 10.1007/s00216-014-7703-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/26/2022]
Abstract
Enzyme-catalyzed reactions play key roles in disease pathology, thus making them relevant subjects of therapeutic inhibitor screening experiments. Matrix-assisted laser desorption/ionization (MALDI) assays have been demonstrated to be able to replace established screening approaches. They offer increased sample throughput, but care must be taken to avoid instrumental bias from differences in ionization efficiencies. We compared a MALDI-triple-quadrupole (QqQ) method for the Dyrk1A peptide substrate woodtide to LC-MS, liquid chromatography with ultraviolet detection (LC-UV), luminescence, and radiometric assays. MALDI measurements were performed on a MALDI-QqQ instrument in the multiple-reaction monitoring mode. Different MALDI conditions were investigated to address whether matrix type, sample support, and MRM- or SIM-based detection conditions can be used to accommodate the molar responses of substrate peptide and its phosphorylated form. UV detection served as a reference method. The impact of MALDI matrix on IC50 values was small, even considering that matrix preparations were used that are known to alleviate response differences. IC50 values determined by MALDI were ca. 2-fold lower than those determined by LC-UV. Although MALDI generated lower ion yields for the phosphorylated peptide than for the peptide substrate, we found that a correction of compound potencies was readily possible using correction factors based on unbiased LC-UV results. A thorough method development delivered a robust assay with excellent performance (Z' > 0.91) that was close to that seen for LC-UV.
Collapse
Affiliation(s)
- David Gode
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | | | | | | |
Collapse
|
3
|
Holzhauser S, Freiwald A, Weise C, Multhaup G, Han CT, Sauer S. Screening und Charakterisierung von Protein-modifizierenden Naturstoffen durch MALDI-Massenspektrometrie bringen starke SIRT1- und p300-Inhibitoren hervor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
4
|
Holzhauser S, Freiwald A, Weise C, Multhaup G, Han C, Sauer S. Discovery and Characterization of Protein‐Modifying Natural Products by MALDI Mass Spectrometry Reveal Potent SIRT1 and p300 Inhibitors. Angew Chem Int Ed Engl 2013; 52:5171-4. [DOI: 10.1002/anie.201207325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/12/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Susanne Holzhauser
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Anja Freiwald
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
| | - Christoph Weise
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Gerd Multhaup
- Fachbereich Biologie, Chemie, Pharmazie/Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3/Thielallee 63, 14195 Berlin (Germany)
| | - Chung‐Ting Han
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73, 14195 Berlin (Germany)
| |
Collapse
|
5
|
Han A, Hosokawa K, Maeda M. Phosphate-affinity electrophoresis on a microchip for determination of protein kinase activity. Electrophoresis 2009; 30:3507-13. [DOI: 10.1002/elps.200900142] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
6
|
Kinumi T, Niki E, Shigeri Y, Matsumoto H. Affinity-tagged phosphorylation assay by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (ATPA-MALDI): application to calcium/calmodulin-dependent protein kinase. J Biochem 2009; 138:791-6. [PMID: 16428308 DOI: 10.1093/jb/mvi178] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based kinase assay using a peptide substrate tagged with a biotinyl group has been developed. The peptide moiety was designed to serve as an efficient substrate for calcium/calmodulin-dependent protein kinase II, based on the in vivo phosphorylation site of phosrestin I, a Drosophila homolog of arrestin. In the assay, the quantitative relationship was determined from the ratio of the peak areas between the two peaks respectively representing the unphosphorylated and the phosphorylated substrate. Attempts to assay phosphorylated peptides directly from the reaction mixture, gave inaccurate results because of the high noise level caused by the presence of salts and detergents. In contrast, after purifying the substrate peptides with the biotin affinity tag using streptavidin-coated magnetic beads, peak areas accurately represented the ratio between the unphosphorylated and phosphorylated peptide. By changing the substrate peptide to a peptide sequence that serves as a kinase substrate, it is expected that an efficient non-radioactive protein kinase assay using MALDI-TOF MS can be developed for any type of protein kinase. We call this technique "Affinity-Tagged Phosphorylation Assay by MALDI-TOF MS (ATPA-MALDI)." ATPA-MALDI should serve as a quick and efficient non-radioactive protein kinase assay by MALDI-TOF MS.
Collapse
Affiliation(s)
- Tomoya Kinumi
- Human Stress Signal Research Center, Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda 563-8577
| | | | | | | |
Collapse
|
7
|
Duncan MW, Roder H, Hunsucker SW. Quantitative matrix-assisted laser desorption/ionization mass spectrometry. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 7:355-70. [PMID: 19106161 DOI: 10.1093/bfgp/eln041] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review summarizes the essential characteristics of matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF MS), especially as they relate to its applications in quantitative analysis. Approaches to quantification by MALDI-TOF MS are presented and published applications are critically reviewed.
Collapse
Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Metabolism and Diabetes, School of Medicine, University of Colorado Denver, Mail Stop 8106, 12801 East 17th Avenue, Aurora, CO 80045, USA.
| | | | | |
Collapse
|
8
|
Parker L, Engel-Hall A, Drew K, Steinhardt G, Helseth DL, Jabon D, McMurry T, Angulo DS, Kron SJ. Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:518-527. [PMID: 18064576 PMCID: PMC2874747 DOI: 10.1002/jms.1342] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Despite advances in methods and instrumentation for analysis of phosphopeptides using mass spectrometry, it is still difficult to quantify the extent of phosphorylation of a substrate because of physiochemical differences between unphosphorylated and phosphorylated peptides. Here we report experiments to investigate those differences using MALDI-TOF mass spectrometry for a set of synthetic peptides by creating calibration curves of known input ratios of peptides/phosphopeptides and analyzing their resulting signal intensity ratios. These calibration curves reveal subtleties in sequence-dependent differences for relative desorption/ionization efficiencies that cannot be seen from single-point calibrations. We found that the behaviors were reproducible with a variability of 5-10% for observed phosphopeptide signal. Although these data allow us to begin addressing the issues related to modeling these properties and predicting relative signal strengths for other peptide sequences, it is clear that this behavior is highly complex and needs to be further explored.
Collapse
Affiliation(s)
- Laurie Parker
- Ludwig Center for Metastasis Research, University of Chicago, Knapp R322, 924 E. 57th Street, Chicago, IL 60637, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Kang JH, Kuramoto M, Tsuchiya A, Toita R, Asai D, Sato YT, Mori T, Niidome T, Katayama Y. Letter: correlation between phosphorylation ratios by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis and enzyme kinetics. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2008; 14:261-265. [PMID: 18756024 DOI: 10.1255/ejms.916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To identify the correlation between the phosphorylation ratios by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) analysis and enzyme kinetics (Km, Vmax, and Vmax/Km) is important to understand whether MALDI-TOF MS can be applied for monitoring the properties of peptides that are substrates of protein kinases. The correlation between phosphorylation ratios and enzyme kinetics was examined using peptides for protein kinase C (PKC) and for 60 kDa phosphoprotein, encoded by the cellular sarcoma gene (c-Src). Phosphorylation ratios, analyzed by MALDI-ToF MS, showed higher correlation coefficient (r = or > +0.7) for Vmax/Km compared with that (r = or < -/+0.6) for Km or Vmax. For ion modes, a higher correlation coefficient between phosphorylation ratios and Vmax/Km was identified in the positive mode (r = or > +0.7) compared to that in the negative mode (r = or < +0.5). These results suggest that MALDI-ToF MS is a useful tool to evaluate Vmax/Km of peptides for protein kinases.
Collapse
Affiliation(s)
- Jeong-Hun Kang
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Ishida A, Kameshita I, Sueyoshi N, Taniguchi T, Shigeri Y. Recent Advances in Technologies for Analyzing Protein Kinases. J Pharmacol Sci 2007; 103:5-11. [PMID: 17202749 DOI: 10.1254/jphs.cp0060026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Most cellular events are regulated by protein phosphorylation mediated by protein kinases, whose malfunction is involved in the etiology of various disorders. The elucidation of the biochemical properties of the protein phosphorylation reaction will lead not only to a better understanding of the signal transduction mechanism, but also to developing new therapeutic agents. In this review, we briefly summarize the technologies to detect or characterize protein kinases with special emphasis on recently developed and/or commercially available techniques.
Collapse
Affiliation(s)
- Atsuhiko Ishida
- Department of Biochemistry, Asahikawa Medical College, Asahikawa 078-8510, Japan
| | | | | | | | | |
Collapse
|
11
|
Parker LL, Schilling AB, Kron SJ, Kent SBH. Optimizing thiophosphorylation in the presence of competing phosphorylation with MALDI-TOF-MS detection. J Proteome Res 2006; 4:1863-6. [PMID: 16212443 PMCID: PMC4568822 DOI: 10.1021/pr050150e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiophosphorylation provides a metabolically stable, chemically reactive phosphorylation analogue for analyzing the phosphoproteome in vitro and in vivo. We developed a MALDI-TOF-MS based assay for optimizing thiophosphopeptide production by a kinase even in the presence of Mg(2+) and ATP. We found that Abl kinase thiophosphorylation rates can be "rescued" using Mn(2+) in the presence of Mg(2+). Under our ideal conditions, titration of Mn(2+) and ATPgammaS in the presence of Mg(2+) allowed relatively rapid, highly specific thiophosphorylation by Abl tyrosine kinase, both as purified enzyme and in complex cell extracts.
Collapse
Affiliation(s)
- Laurie L Parker
- Department of Biochemistry and Molecular Biology, University of Chicago, CIS 201, 929 E. 57 Street, Chicago, IL 60637, USA.
| | | | | | | |
Collapse
|
12
|
Charvat A, Bógehold A, Abel B. Time-Resolved Micro Liquid Desorption Mass Spectrometry: Mechanism, Features, and Kinetic Applications. Aust J Chem 2006. [DOI: 10.1071/ch05249] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Liquid water beam desorption mass spectrometry is an intriguing technique to isolate charged molecular aggregates directly from the liquid phase and to analyze them employing sensitive mass spectrometry. The liquid phase in this approach consists of a 10 µm diameter free liquid filament in vacuum which is irradiated by a focussed infrared laser pulse resonant with the OH-stretch vibration of bulk water. Depending upon the laser wavelength, charged (e.g. protonated) macromolecules are isolated from solution through a still poorly characterized mechanism. After the gentle liquid-to-vacuum transfer the low-charge-state aggregates are analyzed using time-of-flight mass spectrometry. A recent variant of the technique uses high performance liquid chromatography valves for local liquid injections of samples in the liquid carrier beam, which enables very low sample consumption and high speed sample analysis. In this review we summarize recent work to characterize the ‘desorption’ or ion isolation mechanism in this type of experiment. A decisive and interesting feature of micro liquid beam desorption mass spectrometry is that — under certain conditions — the gas-phase mass signal for a large number of small as well as supramolecular systems displays a surprisingly linear response on the solution concentration over many orders of magnitude, even for mixtures and complex body fluids. This feature and the all-liquid state nature of the technique makes this technique a solution-type spectroscopy that enables real kinetic studies involving (bio)polymers in solution without the need for internal standards. Two applications of the technique monitoring enzyme digestion of proteins and protein aggregation of an amyloid model system are highlighted, both displaying its potential for monitoring biokinetics in solution.
Collapse
|
13
|
Wu D, Nair-Gill E, Sher DA, Parker LL, Campbell JM, Siddiqui M, Stock W, Kron SJ. Assaying Bcr-Abl kinase activity and inhibition in whole cell extracts by phosphorylation of substrates immobilized on agarose beads. Anal Biochem 2005; 347:67-76. [PMID: 16236241 PMCID: PMC4562293 DOI: 10.1016/j.ab.2005.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 08/17/2005] [Accepted: 09/03/2005] [Indexed: 11/21/2022]
Abstract
There is a current and increasing demand for simple, robust, nonradioactive assays of protein tyrosine kinase activity with applications for clinical diagnosis and high-throughput screening of potential molecularly targeted therapeutic agents. One significant challenge is to detect and measure the activity of specific kinases with key roles in cell signaling as an approach to distinguish normal cells from cancer cells and as a means of evaluating targeted drug efficacy and resistance in cancer cells. Here, we describe a method in which kinase substrates fused to glutathione-S-transferase and immobilized on glutathione agarose beads are phosphorylated, eluted, and then assayed to detect kinase activity. The activity of recombinant, purified c-Abl kinase or Bcr-Abl kinase in whole cell extracts can be detected with equivalent specificity, sensitivity, and reproducibility. Similarly, inhibition of recombinant c-Abl or Bcr-Abl in cells or cell extracts by imatinib mesylate and other Bcr-Abl targeted kinase inhibitors is readily assayed. This simple kinase assay is sufficiently straightforward and robust for use in clinical laboratories and is potentially adaptable to high-throughput assay formats.
Collapse
Affiliation(s)
- Ding Wu
- Center for Molecular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Evan Nair-Gill
- Center for Molecular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Dorie A. Sher
- Department of Medicine and Cancer Research Center, University of Chicago, Chicago, IL 60637, USA
| | - Laurie L. Parker
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jennifer M. Campbell
- Center for Molecular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mariah Siddiqui
- Department of Medicine and Cancer Research Center, University of Chicago, Chicago, IL 60637, USA
| | - Wendy Stock
- Department of Medicine and Cancer Research Center, University of Chicago, Chicago, IL 60637, USA
| | - Stephen J. Kron
- Center for Molecular Oncology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Corresponding author. Fax: +1 773 702 4394
| |
Collapse
|
14
|
Bilati U, Pasquarello C, Corthals GL, Hochstrasser DF, Allémann E, Doelker E. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for quantitation and molecular stability assessment of insulin entrapped within PLGA nanoparticles. J Pharm Sci 2005; 94:688-94. [PMID: 15668947 DOI: 10.1002/jps.20266] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was evaluated for both qualitative and quantitative analysis of insulin entrapped within poly(D,L-lactic-co-glycolic acid) nanoparticles. Quantitation was performed by adding an internal standard (arg-insulin) to defined and unknown sample solutions, in order to reduce point-to-point and sample-to-sample variability. The ratio of the peak height of insulin to the peak height of arg-insulin was plotted against the insulin concentration. In this way, an excellent linear relationship was found (R2 > 0.99). This method of quantitation was compared with classical UV spectroscopy and reverse-phase high-performance liquid chromatography measurements. All methods provided close final drug loading values for the insulin-loaded nanoparticle batches tested. Additionally, with respect to molecular stability, covalent insulin dimers were found only at trace levels in those nanoparticles. Compared with other methods, MALDI-TOF MS is a valuable tool for the characterization of proteins from nanoparticles, because no extensive extraction and complex sampling procedures are required.
Collapse
Affiliation(s)
- Ugo Bilati
- School of Pharmacy, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | | | | | | | | | | |
Collapse
|
15
|
Liesener A, Karst U. Monitoring enzymatic conversions by mass spectrometry: a critical review. Anal Bioanal Chem 2005; 382:1451-64. [PMID: 16007447 DOI: 10.1007/s00216-005-3305-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 05/11/2005] [Accepted: 05/13/2005] [Indexed: 10/25/2022]
Abstract
This review highlights recent advances in the application of electrospray ionisation and matrix-assisted laser desorption/ionisation mass spectrometry (MS) to study enzymatic reactions. Several assay schemes for different fields of application are presented. The employment of MS as a means of detection in pre-steady-state kinetic studies by rapid-mixing direct analysis and rapid-mixing quench flow techniques is discussed. Several steady-state kinetic studies of a broad range of different enzymatic systems are presented as well as enzyme inhibition studies for various target enzymes. As a promising new development multiplex assays, which monitor the conversion of several substrates simultaneously in one experiment, are described. This assay type has been used for competition studies, enzymatic activity screenings and for diagnostic purposes in clinical chemistry. Generally, it can be concluded that mass spectrometry offers an intriguing alternative as detection methodology in enzymatic bioassays. Its applicability for the monitoring the conversion of naturally occurring substrates and its overall versatility make MS an especially promising tool for the study of enzyme-catalysed processes.
Collapse
Affiliation(s)
- André Liesener
- Chemical Analysis Group and MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500, AE Enschede, The Netherlands
| | | |
Collapse
|
16
|
Fabris D. Mass spectrometric approaches for the investigation of dynamic processes in condensed phase. MASS SPECTROMETRY REVIEWS 2005; 24:30-54. [PMID: 15389863 DOI: 10.1002/mas.20007] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mass spectrometry (MS) offers many advantages over other established spectroscopic techniques employed for the investigation of processes in condensed phase. The sensitivity, specificity, and speed afforded by MS-based methods enable to obtain very valuable insights into the mechanism of complex dynamic processes. Off-line methods rely on quenching to halt the progress of the reaction of interest and allow for the implementation of a broad range of analytical procedures for sample fractionation, isolation, or desalting. On the contrary, on-line methods are designed to carry out the real-time monitoring of dynamic processes through a continuous uninterrupted analysis of reaction mixtures, with the only caveat that the sample solutions be directly amenable to the available ionization technique. The utilization of rapid mixing devices in direct connection with a mass spectrometer or included in off-line schemes provides access to the initial moments of a reaction, which can offer very important information about the reaction mechanism. This report summarizes the different off- and on-line strategies developed to study chemical and biochemical reactions in solution and obtain kinetic/mechanistic information. The merits of the various experimental designs, the characteristics of the different instrumental setups, and the factors affecting time resolution are discussed with the aid of specific examples, which highlight the contributions of MS to the different facets of the investigation of dynamic processes in condensed phase.
Collapse
Affiliation(s)
- Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA.
| |
Collapse
|
17
|
Zeller M, Essmann F, Jänicke RU, Schulze-Osthoff K, König S. A rapid nonradioactive peptide phosphorylation assay. JOURNAL OF EXPERIMENTAL THERAPEUTICS AND ONCOLOGY 2003; 3:59-61. [PMID: 12822511 DOI: 10.1046/j.1359-4117.2003.01074.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Radioactive assays are commonly employed to monitor protein or peptide phosphorylation. They not only have all the disadvantages related to radioactivity, but also require large amounts of sample. An alternative is the use of mass spectrometric peptide mapping with sensitivities in the fmole range. We demonstrate here that desalting is a requirement for reproducible results, and we optimized the method for very hydrophilic peptide substrates. The method is very efficient with respect to time and effort.
Collapse
Affiliation(s)
- Martin Zeller
- Interdisciplinary Center for Clinical Research, Core Group Integrated Functional Genomics, Medical Faculty, University of Münster, Münster, Germany
| | | | | | | | | |
Collapse
|
18
|
Gross JW, Frey PA. Rapid mix-quench MALDI-TOF mass spectrometry for analysis of enzymatic systems. Methods Enzymol 2003; 354:27-49. [PMID: 12418215 DOI: 10.1016/s0076-6879(02)54004-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
|
19
|
|
20
|
Nam HS, Ban E, Yoo E, Yoo YS. Determination of protein phosphorylation by extracellular signal-regulated kinase using capillary electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Chromatogr A 2002; 976:79-85. [PMID: 12462598 DOI: 10.1016/s0021-9673(02)01148-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Extracellular signal-regulated kinase (ERK) is a key regulatory enzyme mediating cell responses to mitogenic stimulation and is one of the key components in linking growth factor receptor activation to serine/threonine protein phosphorylation processes. Phosphorylation reaction by ERK plays an important role in many signal transduction pathways. ERK phosphorylates numerous substrates such as MBP, microtubule-associated protein 2 (MAP2) and nuclear protein. In particular, MBP is a substrate commonly employed for the detection of ERK activity and contains the consensus primary sequence PRT97P. In this paper, we compared the degree of the phosphorylation reaction of MBP substrate peptides by ERK with the three different MBP substrate peptides, MBP1(KNIVTPRTPPPSQGK), MBP2(VPRTPGGRR) and MBP3(APRTPGGRR) in order to select an efficient substrate peptide for phosphorylation reaction by ERK. The results showed that the MBP3 peptide is the most efficient substrate for phosphorylation reaction by ERK. Using MBP3 peptide, the phosphorylation reaction of MBP by ERK was monitored with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and capillary electrophoresis (CE). Our results demonstrate the feasibility of the CE method, the method being a simple and reliable technique in determining and characterizing various kinds of enzyme reaction especially including kinase enzymes.
Collapse
Affiliation(s)
- Hui-Sun Nam
- Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul 130-650, South Korea
| | | | | | | |
Collapse
|
21
|
Kokko KP, Dix TA. Monitoring neurotensin[8-13] degradation in human and rat serum utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2002; 308:34-41. [PMID: 12234461 DOI: 10.1016/s0003-2697(02)00235-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method was developed to quantify neurotensin (NT) fragment [8-13] and a novel NT[8-13] derivative, KK1, in human and rat serum utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The method allows for simultaneous quantification of the major NT[8-13] metabolite, NT[9-13] (according to molecular mass), and detection of the major KK1 metabolite, KK1M (according to molecular mass). The degradation rates of NT[8-13] and KK1 were calculated to be 24.1+/-1.0 and 193+/-8min in human serum and 5.90+/-0.22 and 153+/-4min in rat serum, respectively. The method utilizes a novel sample drying technique and spectrum acquisition protocol. In addition, an internal standard dissimilar in structure to the analytes was used. This method may be broadly applicable to the quantification of NT[8-13] and other peptide analogues of varying structure.
Collapse
Affiliation(s)
- Kyle P Kokko
- Department of Pharmaceutical Sciences, Medical University of South Carolina, 280 Calhoun Street, P.O. Box 250140, Charleston 29425-2303, USA
| | | |
Collapse
|
22
|
Niwayama S, Kurono S, Matsumoto H. Synthesis of d-labeled N-alkylmaleimides and application to quantitative peptide analysis by isotope differential mass spectrometry. Bioorg Med Chem Lett 2001; 11:2257-61. [PMID: 11527710 DOI: 10.1016/s0960-894x(01)00452-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
d-Labeled N-alkylmaleimides have been prepared for specific modification of the terminal SH groups of cysteine residues in proteins or peptides. These reagents are useful tools for quantitative analysis of peptides by stable isotope differential mass spectrometry.
Collapse
Affiliation(s)
- S Niwayama
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071, USA.
| | | | | |
Collapse
|
23
|
Wind M, Wesch H, Lehmann WD. Protein phosphorylation degree: determination by capillary liquid chromatography and inductively coupled plasma mass spectrometry. Anal Chem 2001; 73:3006-10. [PMID: 11467547 DOI: 10.1021/ac010066s] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary liquid chromatography (muLC) interfaced to inductively coupled plasma mass spectrometry (ICPMS) is introduced as a new micromethod to determine the phosphorylation degree in phosphoproteins and phosphopeptides containing cysteine and/or methionine residues. The stoichiometric phosphorus to sulfur (31P to 32S) ratio is experimentally determined by muLC-ICPMS and converted into the degree of phosphorylation using protein/ peptide sequence information. The method is applied to the phosphoproteins beta-casein, beta-casein, and recombinant protein kinase A catalytic subunit and to synthetic phosphopeptides. The accurate data obtained by muLC-ICPMS allow quantitative assessment of the compound-specific discrimination of the electrospray ionization process between nonphosphorylated and phosphorylated proteins and peptides.
Collapse
Affiliation(s)
- M Wind
- Central Spectroscopy and Department of Biophysics, German Cancer Research Center (DKFZ), Heidelberg
| | | | | |
Collapse
|
24
|
Chen J, Qi Y, Zhao R, Zhou GW, Zhao ZJ. Assay of protein tyrosine phosphatases by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal Biochem 2001; 292:51-8. [PMID: 11319817 DOI: 10.1006/abio.2001.5071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A nonradioactive assay for protein tyrosine phosphatases (PTPs), employing a tyrosine-phosphorylated peptide as a substrate, has been developed and applied to analyze purified enzymes, cell extracts, and immunoprecipitates. The reaction was followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in a linear and positive ion mode with delayed extraction. MALDI-TOF MS detects a loss of peptide mass by 80 Da as a result of dephosphorylation and, more importantly, it yields phospho-peptide to dephosphorylated product peak intensity ratios proportional to their concentration ratios. A strong bias of the MALDI-TOF MS toward detection of the non-phospho-peptide allows accurate detection of small fractions of dephosphorylation. The method is highly sensitive and reproducible. It can be applied to general assays of protein phosphatases with various phospho-peptides as substrates.
Collapse
Affiliation(s)
- J Chen
- Division of Hematology/Oncology, Vanderbilt University, Nashville, Tennessee 37232-6305, USA
| | | | | | | | | |
Collapse
|
25
|
Houston CT, Taylor WP, Widlanski TS, Reilly JP. Investigation of enzyme kinetics using quench-flow techniques with MALDI-TOF mass spectrometry. Anal Chem 2000; 72:3311-9. [PMID: 10939405 DOI: 10.1021/ac991499m] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry is combined off-line with rapid chemical quench-flow methods to investigate the pre-steady-state kinetics of a protein-tyrosine phosphatase (PTPase). PTPase kinetics are generally interrogated spectrophotometrically by the employment of an artificial, chromophoric substrate. However, that methodology places a constraint on the experiment, hampering studies of natural, biochemically relevant substrates that do not incorporate a chromophore. The mass spectrometric assay reported herein is based on the formation of a covalent phosphoenzyme intermediate during substrate turnover. This species is generated in the reaction regardless of the substrate studied and has a molecular weight 80 Da greater than that of the native enzyme. By following the appearance of this intermediate in a time-resolved manner, we can successfully measure pre-steady-state kinetics, regardless of the incorporation of a chromophore. The strengths of the mass-spectrometric assay are its uniform response to all substrates, simple and direct detection of covalent enzyme-substrate intermediates, and facile identification of enzyme heterogeneities that may affect enzymatic activity.
Collapse
Affiliation(s)
- C T Houston
- Department of Chemistry, Indiana University, Bloomington 47405, USA
| | | | | | | |
Collapse
|
26
|
Matsumoto H, Kahn ES, Komori N. The emerging role of mass spectrometry in molecular biosciences: studies of protein phosphorylation in fly eyes as an example. NOVARTIS FOUNDATION SYMPOSIUM 1999; 224:225-44; discussion 244-8. [PMID: 10614054 DOI: 10.1002/9780470515693.ch13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Modern mass spectrometry (MS) streamlined with two-dimensional gel electrophoresis, in-gel digestion and HPLC-interfaced electrospray ionization quadrupole MS or matrix-assisted laser desorption ionization time-of-flight MS enables us to analyse proteins at a minuscule scale. We present here two examples of MS applications in which (1) we identified the in vivo phosphorylation site of Drosophila arrestin, phosrestin I (PRI), and (2) we revealed the identity of an 80 kDa phosphoprotein (80K) in Drosophila eyes to be the InaD gene product, a member of the PDZ domain proteins. Available evidence suggests that PRI quenches the activation of rhodopsin and that the InaD protein adjusts photoreceptor responsiveness by assembling/disassembling components involved in photoreceptor transduction in flies. PRI undergoes a reversible phosphorylation at a single site, and 80K at multiple sites. The phosphorylation states of PRI and 80K depend on the intensity and/or duration of light stimuli. From these results we postulate that these proteins function as a molecular switch adjusting the signalling cascade through phosphorylation. The combination of two-dimensional gel electrophoresis with MS will be a powerful tool for detailed investigation of such complex switching processes. The techniques described here can be applied also to other complex signalling systems.
Collapse
Affiliation(s)
- H Matsumoto
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73104, USA
| | | | | |
Collapse
|
27
|
Abstract
Oxidized N-beta-Ala-L-His (L-carnosine) emitted low-level CL. The CL specificity was shown by experiments with L-carnosine from six separate vendors, several L-carnosine-like compounds, and nine different oxidizers. Purity of L-carnosine samples was analysed by RP-HPLC-MS, (1)H-NMR, MALDI-TOF-MS and ESI-MS. L-Carnosine CL magnitude varied with source; consequently, detection sensitivity was 5-100 nmol. CL of L-anserine (N-beta-Ala-1-methyl-L-His) was equal to or less than L-carnosine, depending upon oxidizer. H(5)IO(6) (2 mmol/L) in 11 mmol/L NaOH or 20 mmol/L K(3)Fe(CN)(6) + 10 mmol/L H(2)O(2) in 100 mmol/L NaOH were oxidizers of choice. Scavengers of (.)OH(-) radical quenched CL. Kinetic studies revealed a bi-phasic CL comprising a short-lived (<1 s) 'flash' and then prolonged ( approximately 2000 s) 'glow'. A structural basis and mechanism of L-carnosine CL are discussed. L-Carnosine CL could be useful for monitoring its level in biological samples.
Collapse
Affiliation(s)
- K E Achyuthan
- ZymeTx Inc, 800 Research Parkway, Suite #100, Oklahoma City, OK 73104, USA.
| |
Collapse
|