Mass spectrometry data systems

A full description of a mass spectrometry data system is beyond the scope of this present text, but its major roles may be considered to be the following ... 

CLP = contract laboratory program EC = electron capture detection FSCC-MS/DS = fused silica capillary, mass spectrometry/data system GC = gas chromatography HPLC-UV = high-resolution liquid chromatography - ultraviolet detection 2-NP = 2-nitrophenol 4-NP = 4-nitrophenol... 

The well-done mass spectrometry data systems all have isotope pattern modeling programs built in. A number of other stand-alone simulation programs are also available. 

Browne, D. Thompson, T. Mole, D. McDowall, R.D. Some Experiences with a Mass Spectrometry Data System Validation, Chromatographia 55(Suppl S), S75-S78 (2002). 

New techniques such as Py/GC/MS/DS (pyrolysis/gas chromatography/mass spectrometry-data system) and Py/MS/DS have been applied for detection and structural elucidation of complex organic compounds. 

The Chem Master Workstation is a gas chromatography and gas chromatography-mass spectrometry data-processing system that speeds the flow of data through the laboratory and provides essential quality-assurance and quality-control review. It is a PC-based integrated hardware/ software system that converts gas chromatographic and gas chromatography-mass spectrometric data into reliable analytical reports. 

Mass Spectrometry (MS), A Hewlett-Packard 5930A mass spectro-meter was interi aced with a Tracor 222 GC. The ionization potential was 70 eV and the scanning limits were 33 to 450 amu. Scanning and data processing were accomplished with a FINNIGAN/INCOS 2300 mass spectrometer data system. A novel injection system (18) was used in place of the standard injection port in conjunction with the GC/MS system. 

An important, but not widely recognized effect in electron transfer chemistry is the phenomenon that the thermochemical stability order of several tautomeric systems can be inverted upon one-electron oxidation. Hitherto, most of the data stem from gas-phase measurements (photoelectron and mass spectrometry data) or from calculations at several levels of theory (Table 2). While the explicit numbers still differ for each method they all agree on the inversion of the stability order for keto/enol, alkine/allene, imine/enamine, nitrile/isonitrile and aldimine/aminocarbene pairs. One-electron reduction, on the other hand, does not necessarily lead to a thermochemical stability inversion, as demonstrated in the case of acetaldehyde 7cthenol [41]. 

The option for data migration is to assess if it is technically feasible to migrate data. The supplier of the mass spectrometry software systems (Applied Biosystems/MDS Sciex) provides conversion programs to allow a user to migrate electronic records from the Macintosh to the Analyst system. Conversion is necessary as the file formats are completely different between the Macintosh and Windows NT environments. 

Although individual laboratories find it useful to compile their own reference library files, access to very large collections of mass spectra and to published data [55] is essential. A compilation of many thousands of spectra by the Aldermaston Mass Spectrometry Data Centre and the Division of Computer Research and Technology at the National Institutes of Health [56-58] has been made available commercially. The file can be searched in a number of ways using an interactive conversational mass spectral search system via a teletype and acoustic link over telephone lines. 

Figure 3 Schematic drawing showing the immunoaffinity chromatography/reverse-phase chromatography/atmospheric pressure ionization mass spectrometry experiment. System components are represented as follows P, HPLC pump IAC, immunoaffinity column HPLC, analytical column MS, mass spectrometer with atmospheric pressure ionization interface DS, data system and W, waste. Switching valves are represented as .

Gas Chromatography-Mass Spectrometry. A Finnigan MAT 4500 series quadrupole gas chromatograph/mass spectrometer/data system equipped with the same capillary column and using the same temperature program described in the previous section was employed. Helium was used as the carrier gas at an average linear velocity of 47.7 cm/sec (30°C). Injector temperature was 220°C, and the ion source temperature was 180°C. The outlet end of the fused silica column was inserted directly into the ion source block, which was maintained at approximately 180°C. 

Meteor can be interfaced with the MetaboLynx mass spectrometer software from Waters Corporation to integrate mass spectrometry data from metabolism studies directly. MetaboLynx is part of the Waters MassLynx Application Managers, a suite of mass spectrometry instrument software [16]. It is designed for automated metabolism studies with data from LC/MS or LC/MS/MS time-of-flight (TOP) experiments. MetaboLynx is able to detect peaks in an LC/MS data file resulting from in vitro or in vivo biotransformation and provides a list of elemental formulae for unidentified components in a mass spectrum. Meteor uses these data to filter the list of predicted metabolites. System requirements are similar to DEREK for Windows. 

Bottom-up proteomics. This strategy relies on peptide-level information, such as mass or sequence, to identify a protein. Cnrrently, this strategy dominates proteomics research. In this approach, the protein is digested, typically with trypsin, and the digest is analyzed with an appropriate mass spectrometry system to obtain the peptide masses and sequences. The database search with mass spectrometry data characterizes the protein. More details of the mass spectrometry platforms used in this approach are provided in the following sections. 

JICST/JOIS. The Japan Information Center for Science and Technology (fICST) Mass Spectral Database is accessible to users in Japan through the JICST Eactual Database System (fOlS-E). The database uses the NIST/EPA/ MSCD data collection supplemented by spectra from the Mass Spectrometry Society of Japan (84). 

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