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Gao R, Yu Q, Shen Y, Chu Q, Chen G, Fen S, Yang M, Yuan L, McClements DJ, Sun Q. Production, bioactive properties, and potential applications of fish protein hydrolysates: Developments and challenges. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.02.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Dreesen R, Capt A, Oberdoerfer R, Coats I, Pallett KE. Characterization and safety evaluation of HPPD W336, a modified 4-hydroxyphenylpyruvate dioxygenase protein, and the impact of its expression on plant metabolism in herbicide-tolerant MST-FGØ72-2 soybean. Regul Toxicol Pharmacol 2018; 97:170-185. [PMID: 29894735 DOI: 10.1016/j.yrtph.2018.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/09/2018] [Accepted: 06/05/2018] [Indexed: 01/29/2023]
Abstract
By transgenic expression technology, a modified 4-hydroxyphenylpyruvate dioxygenase enzyme (HPPD W336) originating from Pseudomonas fluorescens is expressed in MST-FGØ72-2 soybean to confer tolerance to 4-benzoyl isoxazole and triketone type of herbicides. Characterization and safety assessment of HPPD W336 were performed. No relevant sequence homologies were found with known allergens or toxins. Although sequence identity to known toxins showed identity to HPPD proteins annotated as hemolysins, the absence of hemolytic activity of HPPD W336 was demonstrated in vitro. HPPD W336 degrades rapidly in simulated gastric fluid. The absence of toxicity and hemolytic potential of HPPD W336 was confirmed by in vivo studies. The substrate spectrum of HPPD W336 was compared with wild type HPPD proteins, demonstrating that its expression is unlikely to induce any metabolic shifts in soybean. The potential effect of expression of HPPD W336 on metabolic pathways related to tyrosine was investigated by comparing seed composition of MST-FGØ72-2 soybean with non-genetically modified varieties, demonstrating that expression of HPPD W336 does not change aromatic amino acid, homogentisate and tocochromanol levels. In conclusion, HPPD W336 was demonstrated to be as safe as other food proteins. No adverse metabolic effects were identified related to HPPD W336 expression in MST-FGØ72-2 soybean.
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Affiliation(s)
- Rozemarijn Dreesen
- Bayer CropScience N.V. - Innovation Center, Tech Lane Ghent Science Park 38, B-9052, Gent, Belgium.
| | - Annabelle Capt
- Bayer S.A.S., Bayer CropScience, 355 rue Dostoïevski, 06903, Sophia Antipolis, France.
| | - Regina Oberdoerfer
- Bayer A.G., CropScience Division, Alfred-Nobel-Straße 50, 40789, Monheim, Germany.
| | - Isabelle Coats
- Bayer CropScience L.P., 2 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - Kenneth Edward Pallett
- Bayer CropScience N.V. - Innovation Center, Tech Lane Ghent Science Park 38, B-9052, Gent, Belgium.
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Farmer DR, Edrington TC, Kessenich CR, Wang C, Petrick JS. Improving insect control protein activity for GM crops: A case study demonstrating that increased target insect potency can be achieved without impacting mammalian safety. Regul Toxicol Pharmacol 2017; 89:155-164. [DOI: 10.1016/j.yrtph.2017.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023]
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Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone. Anal Chim Acta 2016; 935:187-96. [DOI: 10.1016/j.aca.2016.06.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/02/2016] [Accepted: 06/16/2016] [Indexed: 11/19/2022]
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Lou X, de Waal BFM, Milroy LG, van Dongen JLJ. A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:766-770. [PMID: 26259660 DOI: 10.1002/jms.3587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin-layer sample preparation method that significantly reduces the analyte suppression effect (ASE). In our method, analytes are deposited on top of the surface of matrix preloaded on the MALDI plate. To prevent embedding of analyte into the matrix crystals, the sample solution were prepared without matrix and efforts were taken not to re-dissolve the preloaded matrix. The results with model mixtures of peptides, synthetic polymers and lipids show that detection of analyte ions, which were completely suppressed using the conventional dried-droplet method, could be effectively recovered by using our method. Our findings suggest that the incorporation of analytes in the matrix crystals has an important contributory effect on ASE. By reducing ASE, our method should be useful for the direct MALDI MS analysis of multicomponent mixtures.
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Affiliation(s)
- Xianwen Lou
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Bas F M de Waal
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Joost L J van Dongen
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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Samperi R, Capriotti AL, Cavaliere C, Colapicchioni V, Chiozzi RZ, Laganà A. Food Proteins and Peptides. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00006-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Purification, characterization and safety assessment of the introduced cold shock protein B in DroughtGard maize. Regul Toxicol Pharmacol 2014; 71:164-73. [PMID: 25545317 DOI: 10.1016/j.yrtph.2014.12.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 11/21/2022]
Abstract
DroughtGard maize was developed through constitutive expression of cold shock protein B (CSPB) from Bacillus subtilis to improve performance of maize (Zea mays) under water-limited conditions. B. subtilis commonly occurs in fermented foods and CSPB has a history of safe use. Safety studies were performed to further evaluate safety of CSPB introduced into maize. CSPB was compared to proteins found in current allergen and protein toxin databases and there are no sequence similarities between CSPB and known allergens or toxins. In order to validate the use of Escherichia coli-derived CSPB in other safety studies, physicochemical and functional characterization confirmed that the CSPB produced by DroughtGard possesses comparable molecular weight, immunoreactivity, and functional activity to CSPB produced from E. coli and that neither is glycosylated. CSPB was completely digested with sequential exposure to pepsin and pancreatin for 2 min and 30 s, respectively, suggesting that CSPB will be degraded in the mammalian digestive tract and would not be expected to be allergenic. Mice orally dosed with CSPB at 2160 mg/kg, followed by analysis of body weight gains, food consumption and clinical observations, showed no discernible adverse effects. This comprehensive safety assessment indicated that the CSPB protein from DroughtGard is safe for food and feed consumption.
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Sandoval W. Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Analysis of Peptides. ACTA ACUST UNITED AC 2014; 77:16.2.1-16.2.11. [DOI: 10.1002/0471140864.ps1602s77] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wendy Sandoval
- Department of Protein Chemistry, Genentech South San Francisco California
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Kannen H, Hazama H, Kaneda Y, Fujino T, Awazu K. Development of laser ionization techniques for evaluation of the effect of cancer drugs using imaging mass spectrometry. Int J Mol Sci 2014; 15:11234-44. [PMID: 24968266 PMCID: PMC4139779 DOI: 10.3390/ijms150711234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/02/2014] [Accepted: 06/09/2014] [Indexed: 12/31/2022] Open
Abstract
Recently, combined therapy using chemotherapy and photodynamic therapy (PDT) has been proposed as a means of improving treatment outcomes. In order to evaluate the efficacy of combined therapy, it is necessary to determine the distribution of the anticancer drug and the photosensitizer. We investigated the use of imaging mass spectrometry (IMS) to simultaneously observe the distributions of an anticancer drug and photosensitizer administered to cancer cells. In particular, we sought to increase the sensitivity of detection of the anticancer drug docetaxel and the photosensitizer protoporphyrin IX (PpIX) by optimizing the ionization-assisting reagents. When we used a matrix consisting of equal weights of a zeolite (NaY5.6) and a conventional organic matrix (6-aza-2-thiothymine) in matrix-assisted laser desorption/ionization, the signal intensity of the sodium-adducted ion of docetaxel (administered at 100 μM) increased about 13-fold. Moreover, we detected docetaxel with the zeolite matrix using the droplet method, and detected PpIX by fluorescence and IMS with α-cyano-4-hydroxycinnamic acid (CHCA) using the spray method.
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Affiliation(s)
- Hiroki Kannen
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hisanao Hazama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yasufumi Kaneda
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tatsuya Fujino
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa Hachioji, Tokyo 192-0397, Japan.
| | - Kunio Awazu
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Lou X, Fransen M, Stals PJM, Mes T, Bovee R, van Dongen JJL, Meijer EW. Unusual analyte-matrix adduct ions and mechanism of their formation in MALDI TOF MS of benzene-1,3,5-tricarboxamide and urea compounds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1405-1412. [PMID: 23812871 DOI: 10.1007/s13361-013-0672-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/11/2013] [Accepted: 05/05/2013] [Indexed: 06/02/2023]
Abstract
Analyte-matrix adducts are normally absent under typical matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) conditions. Interestingly, though, in the analysis of several types of organic compounds synthesized in our laboratory, analyte-matrix adduct ion peaks were always recorded when common MALDI matrices such as 4-hydroxy-α-cyanocinnamic acid (CHCA) were used. These compounds are mainly those with a benzene-1,3,5-tricarboxamide (BTA) or urea moiety, which are important building blocks to make new functional supramolecular materials. The possible mechanism of the adduct formation was investigated. A shared feature of the compounds studied is that they can form intermolecular hydrogen bonding with matrices like CHCA. The intermolecular hydrogen bonding will make the association between analyte ions and matrix molecules stronger. As a result, the analyte ions and matrix molecules in MALDI clusters will become more difficult to be separated from each other. Furthermore, it was found that analyte ions were mainly adducted with matrix salts, which is probably due to the much lower volatility of the salts compared with that of their corresponding matrix acids. It seems that the analyte-matrix adduct formation for our compounds are caused by the incomplete evaporation of matrix molecules from the MALDI clusters because of the combined effects of enhanced intermolecular interaction between analyte-matrix and of the low volatility of matrix salts. Based on these findings, strategies to suppress the analyte-matrix adduction are briefly discussed. In return, the positive results of using these strategies support the proposed mechanism of the analyte-matrix adduct formation.
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Affiliation(s)
- Xianwen Lou
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
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Characterising microbial protein test substances and establishing their equivalence with plant-produced proteins for use in risk assessments of transgenic crops. Transgenic Res 2012; 22:445-60. [PMID: 23065372 PMCID: PMC3591531 DOI: 10.1007/s11248-012-9658-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/14/2012] [Indexed: 10/30/2022]
Abstract
Most commercial transgenic crops are genetically engineered to produce new proteins. Studies to assess the risks to human and animal health, and to the environment, from the use of these crops require grams of the transgenic proteins. It is often extremely difficult to produce sufficient purified transgenic protein from the crop. Nevertheless, ample protein of acceptable purity may be produced by over-expressing the protein in microbes such as Escherichia coli. When using microbial proteins in a study for risk assessment, it is essential that their suitability as surrogates for the plant-produced transgenic proteins is established; that is, the proteins are equivalent for the purposes of the study. Equivalence does not imply that the plant and microbial proteins are identical, but that the microbial protein is sufficiently similar biochemically and functionally to the plant protein such that studies using the microbial protein provide reliable information for risk assessment of the transgenic crop. Equivalence is a judgement based on a weight of evidence from comparisons of relevant properties of the microbial and plant proteins, including activity, molecular weight, amino acid sequence, glycosylation and immuno-reactivity. We describe a typical set of methods used to compare proteins in regulatory risk assessments for transgenic crops, and discuss how risk assessors may use comparisons of proteins to judge equivalence.
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Ebhardt HA, Xu Z, Fung AW, Fahlman RP. Quantification of the post-translational addition of amino acids to proteins by MALDI-TOF mass spectrometry. Anal Chem 2010; 81:1937-43. [PMID: 19186990 DOI: 10.1021/ac802423d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoacyl-tRNA protein transferases catalyze the post-translational addition of amino acids to proteins. The eubacterial leucyl/phenylalanyl-tRNA-protein transferase (L/F transferase) catalyzes the transfer of leucine or phenylalanine from their respective aminoacylated tRNAs to the N-termini of substrate proteins possessing an N-terminal lysine or arginine amino acid. Conventional assays to quantify L/F transferase activity involve measuring radioactive amino acid incorporation into substrate proteins. We have developed a quantitative matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry procedure to measure the enzymatic activity of L/F transferase. The procedure utilizes stable isotope labeled substrate and internal standard peptides. The method is used to determine the kinetic parameters of k(cat) and K(m) for the enzymatic transfer of phenylalanine and three unnatural amino acid derivatives from an aminoacyl-tRNA to a peptide substrate.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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Morisaki Y, Shiotani Y, Lin L, Chujo Y. Synthesis of PAMAM Dendrimers Possessing [2.2]Paracyclophane on Their Surface. Polym J 2008. [DOI: 10.1295/polymj.pj2008046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Kim JS, Kim JY, Kim HJ. Suppression of matrix clusters and enhancement of peptide signals in MALDI-TOF mass spectrometry using nitrilotriacetic acid. Anal Chem 2007; 77:7483-8. [PMID: 16285704 DOI: 10.1021/ac051152l] [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: 11/28/2022]
Abstract
Matrix clusters and their alkali metal ion adducts suppress peptide signals in the 500-1400 Da range and compromise MALDI-TOF mass spectrometric peptide mass fingerprinting and protein identification. Addition of 7 mM nitrilotriacetic acid to the matrix solution significantly reduced matrix clusters and increased signal-to-noise ratio of peptide signals approximately 5 to 20-fold. As a result, reliability in the identification of femtomole amounts of proteins based on peptide mass fingerprinting and database search was significantly enhanced, leading to a higher score and sequence coverage.
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Affiliation(s)
- Jong-Seo Kim
- Department of Chemistry, Seoul National University, Korea
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A Novel Desalting Method on Target for MALDI-TOF-MS Analysis Based on Fe3O4/TiO2 Nanoparticles. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2007. [DOI: 10.1016/s1872-2040(07)60023-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hileman RE, Bonner HKS, Kaempfe TA, Hammond BG, Glenn KC. Safety assessment of cre recombinase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:8640-7. [PMID: 17061845 DOI: 10.1021/jf061210j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cre recombinase, when used as a tool in agricultural biotechnology, can precisely excise DNA sequences that may be useful in the introduction of a new trait but are not needed in the commercial product. Although the cre genetic material would not be present in the final product, the present studies were performed to assess the safety of Cre recombinase to provide confirmatory evidence of the safe use of Cre-lox technology in agricultural biotechnology. Cre recombinase shares no relevant sequence similarity to known allergens or toxins. When Cre recombinase was exposed to a pH 1.2 solution of simulated gastric fluid lacking pepsin, CD spectroscopy showed that there was a loss of secondary structure and that the protein was no longer active in a functional assay. Cre recombinase was degraded rapidly when exposed to pepsin in a standardized gastric digestion model; therefore, Cre recombinase would not survive the harsh gastric environment. When orally administered to mice as an acute dosage of 53 mg/kg of body weight, no treatment-related adverse findings were observed. These data support the conclusion that human and animal dietary exposure to Cre recombinase pose no known safety concerns; consistent with the fact that bacteriophage P1, the source of the cre gene and expressed protein, is commonly encountered in the environment and in normal enteric bacteria without reports of adverse consequences.
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Tholey A, Heinzle E. Ionic (liquid) matrices for matrix-assisted laser desorption/ionization mass spectrometry-applications and perspectives. Anal Bioanal Chem 2006; 386:24-37. [PMID: 16830111 DOI: 10.1007/s00216-006-0600-5] [Citation(s) in RCA: 233] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 06/06/2006] [Accepted: 06/07/2006] [Indexed: 11/30/2022]
Abstract
A large number of matrix substances have been used for various applications in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The majority of matrices applied in ultraviolet-MALDI MS are crystalline, low molecular weight compounds. A problem encountered with many of these matrices is the formation of hot spots, which lead to inhomogeneous samples, thus leading to increased measurement times and hampering the application of MALDI MS for quantitative purposes. Recently, ionic (liquid) matrices (ILM or IM) have been introduced as a potential alternative to the classical crystalline matrices. ILM are equimolar mixtures of conventional MALDI matrix compounds such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxycinnamic acid (CCA) or sinapinic acid (SA) together with organic bases [e.g., pyridine (Py), tributylamine (TBA) or N,N-dimethylethylenediamine (DMED)]. The present article presents a first overview of this new class of matrices. Characteristic properties of ILM, their influence on mass spectrometric parameters such as sensitivity, resolution and adduct formation and their application in the fields of proteome analysis, the measurement of low molecular weight compounds, the use of MALDI MS for quantitative purposes and in MALDI imaging will be presented. Scopes and limitations for the application of ILM are discussed.
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Affiliation(s)
- Andreas Tholey
- Technische Biochemie, Geb. 1.5, Universität des Saarlandes, 66123 Saarbrücken, Germany.
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Huang YF, Chang HT. Nile Red-Adsorbed Gold Nanoparticle Matrixes for Determining Aminothiols through Surface-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2006; 78:1485-93. [PMID: 16503598 DOI: 10.1021/ac0517646] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes the use of Nile Red-adsorbed gold nanoparticles (NRAuNPs) as selective probes and matrixes for the determination of aminothiols through surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). The binding of three aminothiols-glutathione (GSH), cysteine (Cys), and homocysteine (HCys)-to the surfaces of these NRAuNPs induces their aggregation, which causes asubsequent changes in their color and fluorescence. Because arginine-a non-thiol amino acid-does not induce such aggregation, it is a straightforward process to use the NRAuNPs to selectively concentrate the aminothiols from a solution containing all four of these analytes; we were able to identify the three aminothiols in the precipitate, and arginine in the supernatant, directly through SALDI-MS measurements. Without using this preconcentration approach, the limits of detection (LODs) at a signal-to-noise ratio of 3 were 1.0, 2.0, and 1.3 microM for GSH, Cys, and HCys, respectively. In comparison, selective concentration using the NRAuNPs provided LODs of 25, 54, and 34 nM, for the determinations of GSH, Cys, and HCys, respectively. NRAuNP matrixes provide a number of advantages over the use of conventional organic matrixes (e.g., 2,5-dihydroxybenzoic acid), such as ease of preparation, selectivity, sensitivity, and repeatability. We validated the applicability of our method through the analyses of GSH in red blood cells and of Cys in plasma; we believe that this approach has great potential for diagnosis.
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Affiliation(s)
- Yu-Fen Huang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei, Taiwan
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Stemmler EA, Gardner NP, Guiney ME, Bruns EA, Dickinson PS. The detection of red pigment-concentrating hormone (RPCH) in crustacean eyestalk tissues using matrix-assisted laser desorption/ionization-Fourier transform mass spectrometry: [M + Na]+ ion formation in dried droplet tissue preparations. JOURNAL OF MASS SPECTROMETRY : JMS 2006; 41:295-311. [PMID: 16421875 DOI: 10.1002/jms.989] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Red pigment-concentrating hormone (RPCH), an octapeptide found in crustaceans and insects with the sequence pGlu-Leu-Asn-Phe-Ser-Pro-Gly-Trp-NH2, is an N- and C-terminally blocked uncharged peptide. These structural features are shared with many members of the larger adipokinetic hormone (AKH)/RPCH peptide family in insects. We have applied vacuum UV matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron mass spectrometry (FTMS) to the direct analysis of crustacean sinus gland tissues, using 2,5-dihydroxybenzoic acid (DHB) as the MALDI matrix, and have found that RPCH is detected in the cationized, [M + Na]+, form under conditions where other peptides in the direct tissue spectra are protonated without accompanying [M + Na]+ or [M + K]+ satellite peaks. The [M + H]+ ion for RPCH is not detected in tissue samples or for an RPCH standard, even when care is taken to eliminate metal ions. This behavior is not unprecedented; however, both direct tissue spectra and SORI-CID spectra provide no clues to suggest that the ionizing agent is a metal cation. In this communication, we characterize the MALDI-FTMS ionization and SORI-CID mass spectra of the [M + Na]+ and [M + K]+ ions from RPCH, and report on the detection of this neuropeptide in sinus gland tissues from the lobster Homarus americanus and the kelp crab Pugettia producta. We describe two strategies, an on-probe extraction procedure and a salt-doping approach, that can be applied to previously analyzed MALDI tissue samples to enhance and unmask sodiated peptides that may otherwise be mistaken for novel neuropeptides.
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Hsieh Y, Casale R, Fukuda E, Chen J, Knemeyer I, Wingate J, Morrison R, Korfmacher W. Matrix-assisted laser desorption/ionization imaging mass spectrometry for direct measurement of clozapine in rat brain tissue. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:965-72. [PMID: 16470674 DOI: 10.1002/rcm.2397] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Matrix-assisted laser desorption/ionization hyphenated with quadrupole time-of-flight (QTOF) mass spectrometry (MS) has been used to directly determine the distribution of pharmaceuticals in rat brain tissue slices which might unravel their disposition for new drug development. Clozapine, an antipsychotic drug, and norclozapine were used as model compounds to investigate fundamental parameters such as matrix and solvent effects and irradiance dependence on MALDI intensity but also to address the issues with direct tissue imaging MS technique such as (1) uniform coating by the matrix, (2) linearity of MALDI signals, and (3) redistribution of surface analytes. The tissue sections were coated with various matrices on MALDI plates by airspray deposition prior to MS detection. MALDI signals of analytes were detected by monitoring the dissociation of the individual protonated molecules to their predominant MS/MS product ions. The matrices were chosen for tissue applications based on their ability to form a homogeneous coating of dense crystals and to yield greater sensitivity. Images revealing the spatial localization in tissue sections using MALDI-QTOF following a direct infusion of (3)H-clozapine into rat brain were found to be in good correlation with those using a radioautographic approach. The density of clozapine and its major metabolites from whole brain homogenates was further confirmed using fast high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) procedures.
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Affiliation(s)
- Yunsheng Hsieh
- Drug Metabolism and Pharmacokinetics Department, Schering-Plough Research Institute, Kenilworth, NJ 07033, USA.
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Dashtiev M, Frankevich V, Zenobi R. Signal enhancement in matrix-assisted laser desorption/ionization by doping with Cu(II) chloride. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:289-291. [PMID: 15609376 DOI: 10.1002/rcm.1768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Kjellström S, Jensen ON. Phosphoric Acid as a Matrix Additive for MALDI MS Analysis of Phosphopeptides and Phosphoproteins. Anal Chem 2004; 76:5109-17. [PMID: 15373450 DOI: 10.1021/ac0400257] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphopeptides are often detected with low efficiency by MALDI MS analysis of peptide mixtures. In an effort to improve the phosphopeptide ion response in MALDI MS, we investigated the effects of adding low concentrations of organic and inorganic acids during peptide sample preparation in 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. Phosphoric acid in combination with 2,5-DHB matrix significantly enhanced phosphopeptide ion signals in MALDI mass spectra of crude peptide mixtures derived from the phosphorylated proteins alpha-casein and beta-casein. The beneficial effects of adding up to 1% phosphoric acid to 2,5-DHB were also observed in LC-MALDI-MS analysis of tryptic phosphopeptides of B. subtilis PrkC phosphoprotein. Finally, the mass resolution of MALDI mass spectra of intact proteins was significantly improved by using phosphoric acid in 2,5-DHB matrix.
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Affiliation(s)
- Sven Kjellström
- Protein Research Group, Department of Biochemistry & Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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23
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Pinel G, André F, Le Bizec B. Discrimination of recombinant and pituitary-derived bovine and porcine growth hormones by peptide mass mapping. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:407-414. [PMID: 14759125 DOI: 10.1021/jf030536e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Somatotropins, which are used in cattle for growth and lactating performances, are difficult to reliably detect because no direct method exists. Reversed-phase high-performance liquid chromatography (RP-HLC) coupled to electrospray ionization quadrupole mass spectrometry (ESI/MS) has been developed to separate and characterize the N-terminal peptides resulting from tryptic cleavage of natural and recombinant growth hormones from different species (bovine, porcine, and human) and suppliers. Conditions for tryptic digestion were optimized. This technique was found to be optimal to cleave efficiently the N-terminal peptide of the proteins without releasing too much noise from the matrix. Characterization of the peptides through ESI(+)-MS allowed natural and recombinant growth hormones from bovine and porcine species with N-terminal amino acid sequences differing from one amino acid residue to be discriminated. However, the studied human growth hormones had similar primary sequences that did not permit any discrimination between recombinant and natural forms, thus confirming the known identity of these hormones. Protein digestions with pepsin and chymotrypsin were also compared but were not conclusive due to the too small N-terminal peptides released after proteolysis.
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Affiliation(s)
- Gaud Pinel
- LABERCA, Ecole Nationale Vétérinaire de Nantes, Route de Gachet, B.P. 50707, 44307 Nantes Cedex 3, France.
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24
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Henzel WJ, Watanabe C, Stults JT. Protein identification: the origins of peptide mass fingerprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:931-42. [PMID: 12954162 DOI: 10.1016/s1044-0305(03)00214-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Peptide mass fingerprinting (PMF) grew from a need for a faster, more efficient method to identify frequently observed proteins in electrophoresis gels. We describe the genesis of the idea in 1989, and show the first demonstration with fast atom bombardment mass spectrometry. Despite its promise, the method was seldom used until 1992, with the coming of significantly more sensitive commercial instrumentation based on MALDI-TOF-MS. We recount the evolution of the method and its dependence on a number of technical breakthroughs, both in mass spectrometry and in other areas. We show how it laid the foundation for high-throughput, high-sensitivity methods of protein analysis, now known as proteomics. We conclude with recommendations for further improvements, and speculation of the role of PMF in the future.
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Affiliation(s)
- William J Henzel
- Protein Chemistry Department and Bioinformatics Department, Genentech, Inc., South San Francisco, California, USA
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25
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Laugesen S, Roepstorff P. Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:992-1002. [PMID: 12954167 DOI: 10.1016/s1044-0305(03)00262-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A new sample preparation method for MALDI based on the use of a mixture of the two commonly used matrices, DHB and CHCA, is described. The matrix mixture preparation results in increased sequence coverage and spot-to-spot reproducibility for peptide mass mapping compared to the use of the single matrix components. This results in more reliable protein identification in proteomics studies and facilitates automated data acquisition. This method shows better tolerance towards salts and impurities, eliminating the need for pre-purification of the samples. It has also been found to be advantageous for the analysis of intact proteins, and especially for glycoproteins. The mixture allows the presence of rather high concentrations of urea in the sample solutions.
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Affiliation(s)
- Sabrina Laugesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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26
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27
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Vlahou A, Schellhammer PF, Wright GL. Application of a novel protein chip mass spectrometry technology for the identification of bladder cancer-associated biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2003; 539:47-60. [PMID: 15088895 DOI: 10.1007/978-1-4419-8889-8_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Antonia Vlahou
- Department of Microbiology, Eastern Virginia Medical School, Virginia Prostate Center, Norfolk 23510, USA
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28
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He Y, Zhong W, Yeung ES. Multiplexed on-column protein digestion and capillary electrophoresis for high-throughput comprehensive peptide mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 782:331-41. [PMID: 12458016 DOI: 10.1016/s1570-0232(02)00698-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A novel scheme based on multiplexed capillary electrophoresis (CE) has been developed for high-throughput, low-cost and comprehensive peptide mapping. Orthogonal peptide maps of the protein of interest were obtained by using multiple reaction conditions with three different enzymes (trypsin, pepsin, and chymotrypsin), and multiple separation conditions with six zone electrophoresis buffers and two micellar electrokinetic chromatography (MEKC) buffers. Fifteen nanoliters of two protein samples (beta-lactoglobulin A and beta-lactoglobulin B) were separately mixed on-column and digested independently at 37 degrees C for 10 min to produce peptides in a 20-capillary system. The resulting peptides were detected simultaneously at 214 nm by a photodiode array detector. The overall analysis time from reaction to detection was about 40 min.
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Affiliation(s)
- Yan He
- Ames Laboratory, US Department of Energy, Iowa 50011, USA
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29
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Sonsmann G, Römer A, Schomburg D. Investigation of the influence of charge derivatization on the fragmentation of multiply protonated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:47-58. [PMID: 11777199 DOI: 10.1016/s1044-0305(01)00328-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The fragmentation of the multiply charged peptides b-chain of bovine insulin and glucagon have been investigated under low energy collision induced dissociation (CID) conditions using an electrospray ion trap mass spectrometer. The influence of charge state, specific amino acids such as aspartate or proline, the location of basic sites, and the derivatization on the fragmentation behavior has been the focus of interest. As a basis for understanding the fragmentation process, the concept of the mobile proton was applied. A set of different derivatives was used to manipulate the sites of protonation of the peptides in order to control and improve the fragmentation behavior. These results can be applied for de novo sequencing, although the sequence-specific fragmentation processes have significant influence on the dissociation behavior of the peptides.
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30
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Distler AM, Allison J. Improved MALDI-MS analysis of oligonucleotides through the use of fucose as a matrix additive. Anal Chem 2001; 73:5000-3. [PMID: 11681479 DOI: 10.1021/ac015550+] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the development of matrix additives, the MALDI-MS analysis of oligonucleotides has improved greatly. When the monosaccharide fucose is combined with the matrix, the homogeneity of the MALDI target, signal strength, and signal duration are increased. The sensitivity of the MALDI experiment increases, allowing for improved detection of components in a complex mixture of oligonucleotides, such as that encountered in sequencing experiments. The addition of fucose to the matrix also causes a reduction in the extent of fragmentation of oligonucleotides.
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Affiliation(s)
- A M Distler
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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31
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32
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Jiang Q, Taupenot L, Mahata SK, Mahata M, O'Connor DT, Miles LA, Parmer RJ. Proteolytic cleavage of chromogranin A (CgA) by plasmin. Selective liberation of a specific bioactive CgA fragment that regulates catecholamine release. J Biol Chem 2001; 276:25022-9. [PMID: 11342539 DOI: 10.1074/jbc.m101545200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromogranin A (CgA), the major soluble protein in catecholamine storage vesicles, serves as a prohormone that is cleaved into bioactive peptides that inhibit catecholamine release, providing an autocrine, negative feedback mechanism for regulating catecholamine responses during stress. However, the proteases responsible for the processing of CgA and release of bioactive peptides have not been established. Recently, we found that chromaffin cells express components of the plasmin(ogen) system, including tissue plasminogen activator, which is targeted to catecholamine storage vesicles and released with CgA and catecholamines in response to sympathoadrenal stimulation, and high affinity cell surface receptors for plasminogen, to promote plasminogen activation at the cell surface. In the present study, we investigated processing of CgA by plasmin and sought to identify specific bioactive CgA peptides produced by plasmin proteolysis. Highly purified human CgA (hCgA) was produced by expression in Escherichia coli and purification using metal affinity chromatography. hCgA was digested with plasmin. Matrix-assisted laser desorption/ionization mass spectrometry identified a major peptide produced with a mass/charge ratio (m/z) of 1546, corresponding uniquely to hCgA-(360-373), the identity of which was confirmed by reverse phase high pressure liquid chromatography and amino-terminal microsequencing. hCgA-(360-373) was selectively liberated by plasmin from hCgA at early time points and was stable even after prolonged exposure to plasmin. The corresponding synthetic peptide markedly inhibited nicotine-induced catecholamine release from pheochromocytoma cells. These results identify plasmin as a protease, present in the local environment of the chromaffin cell, that selectively cleaves CgA to generate a bioactive fragment, hCgA-(360-373), that inhibits nicotinic-mediated catecholamine release. These results suggest that the plasminogen/plasmin system through its interaction with CgA may play a major role in catecholaminergic function and suggest a specific mechanism as well as a discrete CgA peptide through which this effect is mediated.
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Affiliation(s)
- Q Jiang
- Department of Medicine, University of California-San Diego, 3350 La Jolla Village Dr., San Diego, CA 92161, USA
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33
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Friess SD, Zenobi R. Protein structure information from mass spectrometry? Selective titration of arginine residues by sulfonates. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:810-818. [PMID: 11444603 DOI: 10.1016/s1044-0305(01)00257-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Noncovalently bound complexes between basic sites of peptides/proteins and sulfonates are studied using Matrix Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry. Reactive sulfonate dyes such as Cibacron Blue F3G-A are known to bind to protonated amino groups on the exterior of a protein. In this work, we examine a wide range of other sulfonates with distinctly simpler structure and more predictable reactivity. Naphthalene-sulfonic acid derivatives were found to bind to arginine only, as opposed to expected binding to all basic sites (Arg, Lys and His). Detailed control experiments were designed to unambigously confirm this selectivity and to rule out nonspecific adduct formation in the gas phase. The data show that the number of complex adducts found equals the number of accessible arginine sites on the surface of folded peptides and proteins, plus the N-terminus. Lys and His are not complexed nor are buried residues with hindered access. MALDI-MS can therefore provide fast information related to the exposed surface of these biomolecules. Additional titration experiments with 1-anilino-naphthalene-8-sulfonic acid (ANS) revealed that this fluorescent dye, which was often hypothesized to bind to so-called molten globule states of proteins, behaved exactly like all other naphthalene-sulfonic acids. ANS binding thus occurs largely through the sulfonate group.
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Affiliation(s)
- S D Friess
- Department of Chemistry, Swiss Federal Institute of Technology, Zurich
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34
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Gao J, Xu J, Locascio LE, Lee CS. Integrated microfluidic system enabling protein digestion, peptide separation, and protein identification. Anal Chem 2001; 73:2648-55. [PMID: 11403312 DOI: 10.1021/ac001126h] [Citation(s) in RCA: 214] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An integrated platform is presented for rapid and sensitive protein identification by on-line protein digestion and analysis of digested proteins using electrospray ionization mass spectrometry or transient capillary isotachophoresis/capillary zone electrophoresis with mass spectrometry detection. A miniaturized membrane reactor is constructed by fabricating the microfluidic channels on a poly(dimethylsiloxane) substrate and coupling the microfluidics to a poly(vinylidene fluoride) porous membrane with the adsorbed trypsin. On the basis of he large surface area-to-volume ratio of porous membrane media, adsorbed trypsin onto the poly(vinylidene fluoride) membrane is employed for achieving ultrahigh catalytic turnover. The extent of protein digestion in a miniaturized membrane reactor can be directly controlled by the residence time of protein analytes inside the trypsin-adsorbed membrane, the reaction temperature, and the protein concentration. The resulting peptide mixtures can either be directly analyzed using electrospray ionization mass spectrometry or further concentrated and resolved by electrophoretic separations prior to the mass spectrometric analysis. This microfluidic system enables rapid identification of proteins in minutes instead of hours, consumes very little sample (nanogram or less), and provides on-line interface with upstream protein separation schemes for the analysis of complex protein mixtures such as cell lysates.
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Affiliation(s)
- J Gao
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA
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35
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Carr SA, Annan RS. Overview of Peptide and Protein Analysis by Mass Spectrometry. ACTA ACUST UNITED AC 2001; Chapter 10:Unit 10.21. [DOI: 10.1002/0471142727.mb1021s38] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Steven A. Carr
- SmithKline Beecham Pharmaceuticals King of Prussia Pennsylvania
| | - Roland S. Annan
- SmithKline Beecham Pharmaceuticals King of Prussia Pennsylvania
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36
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Henzel WJ, Stults JT. Reversed-phase isolation of peptides. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2001; Chapter 10:Unit 10.14. [PMID: 18265054 DOI: 10.1002/0471142727.mb1014s54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In reversed-phase HPLC, peptides are separated on a hydrophobic stationary phase and eluted with a gradient of increasing organic solvent concentration. Protocols describing the separation of peptides in 5- to 500-pmol quantities via narrow-bore (2-mm-i.d.) or microbore (1-mm-i.d.) columns, as well as for the separation of peptides in quantities <5 pmol are provided in this unit. Capillary HPLC columns require a gradient flow rate of 3 to 5 omponents present in a small sample prior to automated sequencing is possible via the procedures for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and capillary electrophoresis.
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Affiliation(s)
- W J Henzel
- Genentech, Inc., South San Francisco, California
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37
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Henzel WJ, Stults JT. Matrix-assisted laser desorption/ionization time-of-flight mass analysis of peptides. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2001; Chapter 16:Unit 16.2. [PMID: 18429129 DOI: 10.1002/0471140864.ps1602s04] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is one of the most useful techniques for determining the mass of biomolecules, with exceptional capabilities for mass analysis of peptides. Relative to other ionization techniques, it provides high sensitivity and excellent tolerance of salt and other common buffer components. Routine detection limits for peptides are in the subpicomole range. The ions commonly observed are the protonated molecules (M+H(+)), which makes data analysis relatively easy. This overview discusses instrument configuration and calibration, sample preparation, along with specific approaches for analyzing peptide mixtures, synthetic peptides, and chemical modifications of peptides.
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Affiliation(s)
- W J Henzel
- Genentech, Inc., South San Francisco, California, USA
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38
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Wassenberg D, Wuhrer M, Beaucamp N, Schurig H, Wozny M, Reusch D, Fabry S, Jaenicke R. Local variability of the phosphoglycerate kinase-triosephosphate isomerase fusion protein from Thermotoga maritima MSB 8. Biol Chem 2001; 382:693-7. [PMID: 11405233 DOI: 10.1515/bc.2001.082] [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: 11/15/2022]
Abstract
The pgk-tpi gene locus of Thermotoga maritima encodes both phosphoglycerate kinase (PGK) and a bienzyme complex consisting of a fusion protein of PGK with triosephosphate isomerase (TIM). No separate tpi gene for TIM is present in T. maritima. A frame-shift at the end of the pgk gene has been previously proposed as a mechanism to regulate the expression of the two protein variants [Schurig et al., EMBO J. 14 (1995), 442-451]. Surprisingly, the complete T. maritima genome was found to contain a pgk-tpi sequence not requiring the proposed frameshift mechanism. To clarify the apparent discrepancy, a variety of DNA sequencing techniques were applied, disclosing an anomalous local variability in the pgk-tpi fusion region. The comparison of different DNA samples and the mass spectrometric analysis of the amino acid sequence of the natural fusion protein from T. maritima MSB8 confirmed the local variability of the DNA variants. Since not all peptide masses could be assigned, further variations are conceivable, suggesting an even higher heterogeneity of the T. maritima MSB8 strain.
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Affiliation(s)
- D Wassenberg
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
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39
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Wang MZ, Fitzgerald MC. A solid sample preparation method that reduces signal suppression effects in the MALDI analysis of peptides. Anal Chem 2001; 73:625-31. [PMID: 11217772 DOI: 10.1021/ac0009090] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we report on the application of a solid-solid (SS) sample preparation protocol for the MALDI analysis of peptides and multicomponent peptide mixtures. Our results with a series of model peptides indicate that a SS MALDI sample preparation protocol is useful for the analysis of peptides in the 1-3 kDa mass range. MALDI mass spectra recorded for peptides in this size range using a SS sample preparation were of a quality comparable to spectra recorded using a conventional dried-droplet (DD) sample preparation. Our results with several model peptide mixtures indicate that one advantage of a SS sample preparation protocol for the MALDI analysis of peptides is that it can significantly reduce signal suppression effects in multicomponent mixtures. MALDI results obtained using a SS sample preparation protocol are also more reproducible than results obtained using a conventional DD sample preparation protocol.
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Affiliation(s)
- M Z Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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40
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Itagaki Y, Nakajima T. ACYLPOLYAMINES: MASS SPECTROMETRIC ANALYTICAL METHODS FORAraneidaeSPIDER ACYLPOLYAMINES. ACTA ACUST UNITED AC 2000. [DOI: 10.1081/txr-100100314] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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41
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Ekström S, Onnerfjord P, Nilsson J, Bengtsson M, Laurell T, Marko-Varga G. Integrated microanalytical technology enabling rapid and automated protein identification. Anal Chem 2000; 72:286-93. [PMID: 10658321 DOI: 10.1021/ac990731l] [Citation(s) in RCA: 186] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein identification through peptide mass mapping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a standard technique, used in many laboratories around the world. The traditional methodology often includes long incubations (6-24 h) and extensive manual steps. In an effort to address this, an integrated microanalytical platform has been developed for automated identification of proteins. The silicon micromachined analytical tools, i.e., the microchip immobilized enzyme reactor (mu-chip IMER), the piezoelectric microdispenser, and the high-density nanovial target plates, are the cornerstones in the system. The mu-chip IMER provides on-line enzymatic digestion of protein samples (1 microL) within 1-3 min, and the microdispenser enables subsequent on-line picoliter sample preparation in a high-density format. Interfaced to automated MALDI-TOF MS, these tools compose a highly efficient platform that can analyze 100 protein samples in 3.5 h. Kinetic studies on the microreactors are reported as well as the operation of this microanalytical platform for protein identification, wherein lysozyme, myoglobin, ribonuclease A, and cytochrome c have been identified with a high sequence coverage (50-100%).
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Affiliation(s)
- S Ekström
- Department of Cell and Molecular Biology, Lund University, Sweden
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42
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Dai Y, Whittal RM, Li L. Two-layer sample preparation: a method for MALDI-MS analysis of complex peptide and protein mixtures. Anal Chem 1999; 71:1087-91. [PMID: 10079766 DOI: 10.1021/ac980684h] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The analytical performance of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for direct analysis of peptide and protein mixtures is strongly dependent on the sample and matrix preparation. A two-layer sample preparation method is demonstrated to be very effective for analyzing complex mixtures. In this method, the first layer on the MALDI probe is the densely packed matrix microcrystals formed by fast solvent evaporation of a matrix solution. A mixture solution containing both matrix and sample is then deposited onto the first layer to form uniform analyte/matrix micrococrystals. It is found that the addition of matrix to the second-layer sample solution proves to be critical in analyzing mixtures of peptides and proteins covering a broad mass range. The effect of solvent conditions for preparing the second-layer solution is discussed. The application of this method is demonstrated for the analysis of cow's milk where milk proteins as well as peptide fragments produced from proteins by indigenous proteinases are detected. Direct analyses of peptides and proteins from a bacteria extract and crude egg white are also illustrated.
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Affiliation(s)
- Y Dai
- Department of Chemistry, University of Alberta, Edmonton, Canada
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43
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Erdjument-Bromage H, Lui M, Lacomis L, Grewal A, Annan RS, McNulty DE, Carr SA, Tempst P. Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J Chromatogr A 1998; 826:167-81. [PMID: 9871337 DOI: 10.1016/s0021-9673(98)00705-5] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometry occupies a central position in most current protein identification schemes. So-called 'mass fingerprinting' techniques rely on composite mass patterns of proteolytic fragments, or dissociation products thereof, to query databases. Keys to successful analysis of ever smaller amounts are sensitivity and complete spectral information, both of which depend for a large part on proper sample preparation. Clean-up and concentration of peptide mixtures over eppendorf gel loading tips filled with chromatographic media (i.e. 'micro-tips') are believed to be quite useful in this regard. We have studied quantitative and qualitative aspects of polypeptide extraction using these small manual devices. Optimization of sample volume and additives, micro-tip bed volume, and eluent composition and volume, all contribute to effective recovery (approximately 65-70%, on average). Improper digest conditions can, in fact, lead to far bigger losses, suggesting the need for at least trace amounts of Zwittergent 3-16. Of particular interest is our finding that partial fractionation, obtained by two-step micro-tip elution, generally results in more and better signals during subsequent mass analysis. Thus, by using optimized micro-tips, in combination with adequate sample handling and instrumentation, direct mass spectrometric identification can be routinely and successfully done in any resource facility type setting.
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Affiliation(s)
- H Erdjument-Bromage
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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44
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Gray JS, Yang BY, Montgomery R. Heterogeneity of glycans at each N-glycosylation site of horseradish peroxidase. Carbohydr Res 1998; 311:61-9. [PMID: 9821267 DOI: 10.1016/s0008-6215(98)00209-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The tryptic glycopeptides of horseradish peroxidase isozyme c (HRPc) were studied by methylation linkage analysis, exoglycosidase degradation, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOFMS). Over 90% of the predicted tryptic peptides and glycopeptides of HRPc could be identified in the unfractionated digest. Four glycans, namely (Xyl)Man3(Fuc)GlcNAc2 (major species), (Xyl)Man2(Fuc)GlcNAc2, (Xyl)Man3GlcNAc2, and Man3(Fuc)GlcNAc2 (minor species), were observed at all of the N-glycosylation sites and account for greater than 95% of the carbohydrate. Other members of this glycan family, namely (Xyl)xManm(Fuc)f GlcNAc2 (x = 0 or 1, f = 0 or 1, m = 4, 5, 6, or 7), account for the rest of the glycans. Only traces of high mannose-type glycans were detected in HRPc. Two sites, namely those at Asn-57 and Asn-267, were found to be more heterogeneous than the sites at Asn-13, Asn-158, Asn-186, 198 (doubly glycosylated peptide), Asn-214, and Asn-255. Two of the glycopeptides were observed as part of disulfide-linked species. MALDITOFMS confirmed the N-glycosylation sites previously reported [K.G. Welinder, Eur. J. Biochem., 96 (1979) 483-502] and was used to determine the heterogeneity of the glycan pool at each site.
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Affiliation(s)
- J S Gray
- Department of Biochemistry, College of Medicine, University of Iowa, Iowa City 52242, USA
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Nicola AJ, Gusev AI, Proctor A, Hercules DM. Automation of data collection for matrix-assisted laser desorption/ionization mass spectrometry using a correlative analysis algorithm. Anal Chem 1998; 70:3213-9. [PMID: 11013723 DOI: 10.1021/ac980143s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Automation of data collection in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry using a correlative analysis algorithm is demonstrated. This algorithm was employed to compensate for mass spectral jittering in MALDI data collection (e.g., peak shifts along the m/z axis, signal intensity deviations, etc.). Several important parameters for performing correlative analysis, such as the minimum correlation coefficient to be used and number of mass spectra to acquire prior to correlation, have been investigated and optimized. In addition, the correlation algorithm improved mass resolution of low- and high-molecular-weight compounds by as much as a factor of 4. Signal reproducibility in MALDI quantitative analysis also is improved when correlation is employed for data collection. This data collection algorithm can be used in conjunction with other instrumental optimization programs to allow for fully automated MALDI analysis, which is required for the routine applications carried out in many analytical laboratories.
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Affiliation(s)
- A J Nicola
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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MARTÍNEZ CA, HAY* AS. Synthesis of Hyperbranched Oligomers with Activated Aryl Chloride and Phenol Terminal Groups. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 1998. [DOI: 10.1080/10601329808001962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Williamson NA, Raliegh J, Morrice NA, Wettenhall RE. Post-translational processing of rat ribosomal proteins. Ubiquitous methylation of Lys22 within the zinc-finger motif of RL40 (carboxy-terminal extension protein 52) and tissue-specific methylation of Lys4 in RL29. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 246:786-93. [PMID: 9219540 DOI: 10.1111/j.1432-1033.1997.00786.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The complete amino acid sequences of rat and yeast (Saccharomyces cerevisiae) ribosomal proteins derived from precursors containing an N-terminal ubiquitin or ubiquitin-like sequence (C-terminal extension proteins or CEPs) were determined and investigated for any post-translational modifications by reverse-phase HPLC purification, direct amino acid sequence and mass spectrometric analyses. Covalent modifications were detected in the rat liver proteins RS27a (CEP-80), RL29, RL37 and RL40 (CEP-52), while RS30 (CEP), RL36a, RL39 and RL41 were unmodified. Heterogeneity of RS27a was due to C-terminal truncations, with Lys80 missing from about 20% of the liver RS27a population; C-terminal processing was also detected with RL29 and RL37. No other covalent modifications of liver, brain or thymus RS27a were detected. The rat RL40 structure was identical to the cDNA-predicted sequence except for complete stoichiometric N epsilon-trimethylation of Lys22 within its zinc-finger motif; this modification occurred in the ribosomes of all three rat tissues investigated but not in yeast ribosomes. The methylation characteristics of RL40 were distinct from those of ribosomal protein RL29 in the rat, which was differentially monomethylated at Lys4 in the liver, brain and thymus (27%, > 99% and 95% methylation, respectively). In the case of liver, there was no appreciable difference in the RL29 methylation status of free and membrane-bound ribosomes. The possibilities of an essential role for RL40 methylation in the formation of rat ribosomes, and a distinct regulatory role for RL29 methylation in the rat, are discussed.
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Affiliation(s)
- N A Williamson
- Russell Grimwade School of Biochemistry and Molecular Biology, University of Melbourne, Australia
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Stults JT. Minimizing Peak Coalescence: High-Resolution Separation of Isotope Peaks in Partially Deamidated Peptides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 1997. [DOI: 10.1021/ac970155y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John T. Stults
- Protein Chemistry Department, Genentech, Inc., 460 Point San Bruno Boulevard, South San Francisco, California 94080
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49
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Mackay EA, Ehrhard A, Moniatte M, Guenet C, Tardif C, Tarnus C, Sorokine O, Heintzelmann B, Nay C, Remy JM, Higaki J, Van Dorsselaer A, Wagner J, Danzin C, Mamont P. A possible role for cathepsins D, E, and B in the processing of beta-amyloid precursor protein in Alzheimer's disease. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:414-25. [PMID: 9119007 DOI: 10.1111/j.1432-1033.1997.00414.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Formation of the 4-kDa peptides, which are essential constituents of the extracellular plaques in Alzheimer's disease, involves the sequential cleavage of the amyloid precursor protein (APP) by beta- and gamma-secretases. The carboxy-terminal 99-amino-acid peptide which is liberated from APP by beta-secretase was used as a potential native substrate of the gamma-secretase(s). With the addition of an initiator Met and a FLAG sequence at the C-terminus (betaAPP100-FLAG), it was expressed in Escherichia coli under the control of the T7 promotor. The preferred site(s) of cleavage in the N-terminal 40-amino-acid beta-amyloid peptide and betaAPP100-FLAG by potential gamma-secretase(s) were rapidly identified using matrix-assisted laser-desorption/ionization time-of-flight mass spectroscopy in addition to peptide mapping followed by protein sequence analysis. Since gamma-secretases seem to be active at acidic pH, three cathepsins (D, E and B) were selected for testing. Studies using different detergents indicated that the cleavage preference of cathepsin D for the betaAPP100-FLAG is highly dependent on the surfactant used to solubilize this substrate. All three cathepsins were found to be capable of catabolizing both beta-amyloid peptides and the betaAPP100-FLAG. As cathepsin D was found to cleave the betaAPP100-FLAG in the vicinity of the C-terminus of the beta-amyloid peptides and cathepsin B has a high carboxypeptidase activity at low pH, the possibility cannot be excluded that cathepsins D and B are involved in the amyloidogenic processing of APP.
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Affiliation(s)
- E A Mackay
- Marion Merrell Research Institute, Strasbourg, France
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50
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Courchesne PL, Luethy R, Patterson SD. Comparison of in-gel and on-membrane digestion methods at low to sub-pmol level for subsequent peptide and fragment-ion mass analysis using matrix-assisted laser-desorption/ionization mass spectrometry. Electrophoresis 1997; 18:369-81. [PMID: 9150915 DOI: 10.1002/elps.1150180311] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The success of the mass spectrometric-based approaches for the identification of gel-separated proteins relies upon recovery of peptides, without high levels of ionization-suppressing contaminants, in solvents compatible with the mass spectrometer being employed. We sought to determine whether in-gel or on-membrane digestion provided a significant advantage when low to sub-pmol quantities of gel-separated proteins were analyzed by matrix-assisted laser-desorption/ionization mass spectrometry (MALDI-MS) with respect to the number and size of released peptides. Serial dilutions of five standard proteins of M(r) 17,000 to 97,000 (from 16 pmol to 125 fmol) were electrophoresed and subjected to in-gel digestion (using a microcolumn clean-up protocol, Courchesne, P.L. and Patterson, S. D., BioTechniques, 1997, in press) or on-membrane digestion following blotting to the PVDF-based membranes, Immobilon-P and Immobilon-CD. Peptide maps were able to be obtained for all proteins at the detection limit of each method (Immobilon-P and Immobilon-CD, 0.5 pmol; and in-gel, 125 fmol), and searches of Swiss-Prot or a non-redundant database (> 193000 entries) successfully identified all of the proteins, except beta-casein. Fragment-ion spectra using a curved-field reflector MALDI-MS were obtained from more than one peptide per protein at loads down to 250 fmol (except beta-casein). Using the uninterpreted data, a search of the nonredundant database and a six-way translation of GenBank dbEST (> 2,208,000 entries total) was able to identify myoglobin, carbonic anhydrase II, and phosphorylase b.
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