Computer in mass spectrometry

Chapman, J.R., Computers in Mass Spectrometry, Academic Press, London, 1978. 

Chapman, J. R., "Computers in Mass Spectrometry", Academic Press, New York, 1978. 

Biochemical Apfdications of Mass Spectiometry, G R Waller (Ed X New Yori , Wiley-Interscience, 1972, and SuiipL, 1980 J R Chapman, Computers in Mass Spectrometry. London, Academic Press, 197 ... 

Caprioli, R.M., Continuous-Flow Fast Atom Bombardment Mass Spectrometry, Wiley, New York, 1990. Chapman, J.R., Computers in Mass Spectrometry, Academic Press, London, 1978. 

Chapman Computers in Mass Spectrometry, 1978, book C39D -Ward 1971 C323D... 

CHAPMAN J-R- COMPUTERS IN MASS SPECTROMETRY, P- 150, ACADEMIC PRESS, LONDON (1978)... 

The first applications of computers in mass spectrometry were merely the recording of signals from the multipliers, conversion to spectra, and some data handling. Today, powerful computers are integrated in the spectrometer. They control the scan, define the scan function, set the required voltages, tune the source, and supervise the experiments. The data are stored and interpreted with advanced tools, although at that stage the fully automated procedures are at an end. 

In a recent lecture on the applications of computers in mass spectrometry. Professor Biemann (27) remarked that while on the one hand, mass spectrometry has placed computers into the chemical laboratory in a much more sophisticated manner than other instruments, such as gas chromatography it is true that now we have much more data than before and also much less time to think about them. In fact, he said, some people hardly look at mass spectra any more. 

Most of the previous discussion has concerned addition. Subtraction in binary is very similar, but multiplication is awkward (try it ). For this reason it is quicker for a computer to multiply by carrying out a series of additions. Multiplying 3x5 becomes adding 5 -(- 5 -(- 5. Because each addition is very fast, the time taken for even a large multiplication is very little and still appears instantaneous to us. Only with very large computations does this speed become obvious enough to merit special computers, more powerful than the ones being considered here for use in mass spectrometry. Finally, division is very similar to multiplication, except that a series of subtractions is carried out instead of additions. 

Rarely will it be possible to draw conclusions directly from the raw data of analytical measurements and it is usual for some refinement of the data to be carried out. In its simplest form this could merely comprise background corrections, but it is often much more complex, requiring corrections for a number of factors as in mass spectrometry, X-ray fluorescence and electron probe microanalysis. More complex routines made available by computers include spectrum smoothing, stripping one component from a spectrum or making peak area measurements from chromatograms. 

Electron ionization (earlier called electron impact) (see Chapter 2, Section 2.1.6) occupies a special position among ionization techniques. Historically it was the first method of ionization in mass spectrometry. Moreover it remains the most popular in mass spectrometry of organic compounds (not bioorganic). The main advantages of electron ionization are reliability and versatility. Besides that the existing computer libraries of mass spectra (Wiley/NIST, 2008) consist of electron ionization spectra. The fragmentation mles were also developed for the initial formation of a radical-cation as a result of electron ionization. 

Kurt Varmuza was bom in 1942 in Vienna, Austria. He studied chemistry at the Vienna University of Technology, Austria, where he wrote his doctoral thesis on mass spectrometry and his habilitation, which was devoted to the field of chemometrics. His research activities include applications of chemometric methods for spectra-structure relationships in mass spectrometry and infrared spectroscopy, for structure-property relationships, and in computer chemistry, archaeometry (especially with the Tyrolean Iceman), chemical engineering, botany, and cosmo chemistry (mission to a comet). Since 1992, he has been working as a professor at the Vienna University of Technology, currently at the Institute of Chemical Engineering. 

Proteins are involved in all biological processes and can therefore be considered the functionally most important biological molecules and are crucial for the description of biological systems. The systematic identification and characterization of proteins is called proteomics. A predominant technology platform in proteomics, two-dimensional gel electrophoresis, is used to separate complex protein mixtures allowing individual protein spots on the gel to be identified by computer-operated mass spectrometry. Mass spectrometric data are then processed through a series of computer algorithms such as Mass Lynx and ProteinLynx software to determine the sequence identity of the proteins. 

A computer program, MacSimion, [92] can be used to model the ion trajectories in ion optics after various assumptions. From these considerations it becomes clear that when dealing with several elements any optimization will also lead to compromises. Thus there will always be a difference in performance in mass spectrometry with respect to sensitivity and to the lowest matrix influences between single-element optimization and compromise conditions. 

The immediate future is relatively clear. Continued advances in instrumental techniques, particularly in mass spectrometry and NMR, will make it possible to measure increasingly accurate and precise KIEs on increasingly small amounts of material. At the same time, continued growth in computational power and in the methods of KIE interpretation will make TS analysis an increasingly powerful tool. Currently, one major drawback is that it is too time consuming at present for application in the pharmaceutical industry. TS analysis will have to become much faster to see wide application outside of academia. 

Giger, W., Reinhard, M., Schaffner, C. and Ziircher, F., 1976. Analyses of organic constituents in water by high-resolution gas chromatography in combination with specific detection and computer-assisted mass spectrometry. In L.H. Keith (Editor), Identification and Analysis of Organic Pollutants in Water. Ann Arbor Science, Ann Arbor, Mich., pp. 433—452. 

Studies of PTM have been benefited from the recent advancements in mass spectrometry, the introduction of new software and Internet-based MS data search facilities, computer-assisted topology prediction for a variety of PTMs (visit http // ca.expasy.org/), chemical synthesis of modified peptides and proteins, development of modified peptide specific antibody, in vitro modification techniques, exploitation of other eukaryotic cells such as insect cells for protein expression [4, 5, 16, 32], and progress in affinity purification of modified proteins. 

A more convenient and expeditious means of mass measurement with either design is to interface an electronic detector with an on-line computer that acquires and stores all the data, both m/e values and intensity data, while the spectrum is being scanned. After identifying the m/c ratios of the mass standard, the computer calculates the exact masses of all the unknown peaks from the scanning time between standard and unknown and, within a few minutes, prints on a teletype the exact masses and intensities of all the peaks in the mass spectrum. This is possibly the most elegant technique in mass spectrometry, for it provides the analyst with exact masses which can be used to determine the elemental compositions of all peaks in a mass spectrum. 

The mass spectrometrist sees the digital computer in quite a difEerent light from the theoretical chemist. In mass spectrometry the computer is not generally used to carry out approximations by numerical techniques which vary the parameters. It is mainly cast in the role of mechanical controller, data acquirer and processer, file searcher and as resolver of structures from mass spectra of unknown compounds. 

The present chapter will be mainly devoted to the three other approaches for structure determination, e. g. the Learning Machine Approach (LMA), the Deduction Programming Approach (DPA) and the Heuristic Programming Approach (HPA). Much emphasis will be put on the artificial intelligence approach where the computer is used as a symbol manipulator. The last section will introduce a new departure in the use of a computer for mass spectrometry, the area of theory formation and the proposal of fragmentation mechanisms. 

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