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Manig F, Kuhne K, von Neubeck C, Schwarzenbolz U, Yu Z, Kessler BM, Pietzsch J, Kunz-Schughart LA. The why and how of amino acid analytics in cancer diagnostics and therapy. J Biotechnol 2017; 242:30-54. [DOI: 10.1016/j.jbiotec.2016.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
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Biemann K. Structure Determination of Natural Products by Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:1-19. [PMID: 26161970 DOI: 10.1146/annurev-anchem-071114-040110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.
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Affiliation(s)
- Klaus Biemann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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Biemann K. Laying the groundwork for proteomics: mass spectrometry from 1958 to 1988. J Proteomics 2014; 107:62-70. [PMID: 24448399 DOI: 10.1016/j.jprot.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 01/09/2014] [Indexed: 11/16/2022]
Abstract
The development of mass spectrometric methods in peptide and protein chemistry in the author's laboratory is reviewed, from the first determination of the amino acid sequence of small peptides in the late 1950s to its use for the determination of the primary structure of large proteins by a combination of mass spectrometry and DNA sequencing in the late 1980s. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Affiliation(s)
- Klaus Biemann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Ma B, Johnson R. De novo sequencing and homology searching. Mol Cell Proteomics 2012; 11:O111.014902. [PMID: 22090170 PMCID: PMC3277775 DOI: 10.1074/mcp.o111.014902] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/08/2011] [Indexed: 11/06/2022] Open
Abstract
In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).
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Affiliation(s)
- Bin Ma
- From the ‡School of Computer Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, Canada N2L 3G1
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Penders TJ, Heerma W, Copier H, Dijkstra G, Arens JF. Structure determination of unknown peptides isolated from pig neurohypophysis, by mass spectrometrical analysis: (Of their 2,4-dinitrophenyl peptide methyl esters). ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19660850905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Saund AK, Prashad B, Koul AK, Bachhawat JM, Mathur NK. Carboxylic terminal determination in simpler peptides by selective reduction of carboxylic group by sodium dihydro bis- (2-methoxyethoxy) aluminate. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 2009; 5:7-10. [PMID: 4763355 DOI: 10.1111/j.1399-3011.1973.tb02312.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Gelpí E. From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part I 1965-1984. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:419-435. [PMID: 18338320 DOI: 10.1002/jms.1403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As the title implies, the author undertakes a personal retrospective on the developments that since 1965 have shaped MS and taken it from a position of simply playing a role in protein chemistry to becoming an indispensable tool in proteomics, all in the past 40-year span. The article reviews the MS timeline of events, stopping at various time points where MS made significant contributions to protein chemistry or where the development of new instrumentation for MS represented a major advance for peptide and protein work. Major highlights in the field and their significance for peptide and protein characterization are covered, starting from the pioneering work carried out in the 1960s on peptide derivative formation and sequencing with instrumentation proper of that time, to later work done with triple, quad, and four-sector instruments, and on to the more recent work on the characterization of the proteome with ion traps, time-of-flight (TOF) instruments, and new ionization and tagging techniques.
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Affiliation(s)
- Emilio Gelpí
- Instituto de Investigaciones Biomédicas de Barcelona, CSIC-IDIBAPS, Roselló 161, Barcelona, Spain.
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Wenzel RJ, Matter U, Schultheis L, Zenobi R. Analysis of megadalton ions using cryodetection MALDI time-of-flight mass spectrometry. Anal Chem 2007; 77:4329-37. [PMID: 16013843 DOI: 10.1021/ac0482054] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Presented are initial results from the first commercially available matrix-assisted laser desorption/ionization time-of-flight mass spectrometer specifically designed for the sensitive detection of very high mass ions (macromizer, Comet AG). This new instrument utilizes a 16-element superconducting tunnel junction detector coupled with a fully adjustable gimbal-mounted ion source/focusing region that allows unparalleled sensitivity for detection of singly charged high molecular weight ions. Using this new technology, the singly charged ions in the megadalton region are detected from immunoglobulin M and von Willebrand factor proteins. This detector technology also measures the kinetic energy of the particles impacting the detector, which can be correlated to the charge of the particles. Immunoglobulin G and streptavidin were used to demonstrate the ability of the macromizer instrument to detect high-mass ions and to discern the charge state of the ions.
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Affiliation(s)
- Ryan J Wenzel
- Department of Chemistry, ETH Hönggerberg, CH-8093 Zürich, Switzerland, and Comet AG, CH-3175 Flamatt, Switzerland
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Weinstein B. Separation and determination of amino acids and peptides by gas--liquid chromatography. METHODS OF BIOCHEMICAL ANALYSIS 2006; 14:203-323. [PMID: 5328504 DOI: 10.1002/9780470110324.ch7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Affiliation(s)
- J T Stults
- Protein Chemistry Department, Genentech, Inc., South San Francisco, California
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Biemann K. Four decades of structure determination by mass spectrometry: from alkaloids to heparin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:1254-1272. [PMID: 12443016 DOI: 10.1016/s1044-0305(02)00441-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The early (1950's and 1960's) use of mass spectrometry in natural products chemistry and its evolution to the present significance in biochemistry is recounted. This methodology allowed the facile and speedy determination of the structure of a number of indole alkaloids, such as sarpagine, quebrachamine, and two groups isolated from the roots of Aspidosperma quebracho blanco. At the same time, the first strategy for the sequencing of small peptides by mass spectrometry was demonstrated. It slowly advanced, over a period of two decades, to an important alternative of the ubiquitous automated Edman degradation. Further advances in methodology and instrumentation established mass spectrometry as today's indispensable tool for the characterization of proteins in biochemistry and biology. A new concept of the ionization of highly acidic compounds as the protonated complexes with basic peptides, which allows the accurate determination of the molecular weights of the former, a highly sensitive method for the sequencing of heparin fragments and related sulfated glycosaminoglycans was developed more recently.
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Affiliation(s)
- Klaus Biemann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139-4307, USA.
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Abstract
The application of mass spectrometry (MS) to large biomolecules has been revolutionized in the past decade with the development of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) techniques. ESI and MALDI permit solvent evaporation and sublimation of large biomolecules into the gaseous phase, respectively. The coupling of ESI or MALDI to an appropriate mass spectrometer has allowed the determination of accurate molecular mass and the detection of chemical modification at high sensitivity (picomole to femtomole). The interface of mass spectrometry hardware with computers and new extended mass spectrometric methods has resulted in the use of MS for protein sequencing, post-translational modifications, protein conformations (native, denatured, folding intermediates), protein folding/unfolding, and protein-protein or protein-ligand interactions. In this review, applications of MS, particularly ESI-MS and MALDI time-of-flight MS, to food proteins and peptides are described.
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Affiliation(s)
- H F Alomirah
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, Montreal, Canada
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Chapter 3. Gas chromatography. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/s0167-7306(08)60212-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Chapter 10 Amino acids and oligopeptides. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/s0301-4770(08)61341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Kelley JA, Nau H, Förster HJ, Biemann K. Polypeptide sequencing by a gas chromatograph mass spectrometer computer system: I—generation and derivatization of complex mixtures of oligopeptides. ACTA ACUST UNITED AC 1975. [DOI: 10.1002/bms.1200020607] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Haegele KD, Holzer G, Parr W, Nakagawa SH, Desiderio DM. Mass spectrometry of synthetic oligopeptides N, O-permethylated, N-acetylated derivatives. BIOMEDICAL MASS SPECTROMETRY 1974; 1:175-89. [PMID: 4433736 DOI: 10.1002/bms.1200010307] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Cheesman DW. Structural elucidation of a gonadotropin-inhibiting substance from the bovine pineal gland. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 207:247-53. [PMID: 5444120 DOI: 10.1016/0005-2795(70)90156-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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BARBER M, JOLLES P, VILKAS E, LEDERER E. Determination of amino acid sequences in oligopeptides by mass spectrometry. I. The structure of fortuitine, an acyl-nonapeptide methyl ester. Biochem Biophys Res Commun 1965; 18:469-73. [PMID: 14301445 DOI: 10.1016/0006-291x(65)90775-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Biemann K. Die Anwendung der Massenspektrometrie in der organischen Chemie, insbesondere zur Strukturaufklärung von Naturstoffen. Angew Chem Int Ed Engl 1962. [DOI: 10.1002/ange.19620740303] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Biemann K. The Application of Mass Spectrometry in Organic Chemistry: Determination of the Structure of Natural Products. ACTA ACUST UNITED AC 1962. [DOI: 10.1002/anie.196200981] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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BAKKE JE, CLAYTON RA. Reductive deacylation of cephalins with lithium borohydride. Biochem Biophys Res Commun 1961; 5:176-8. [PMID: 13686146 DOI: 10.1016/0006-291x(61)90105-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
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