Mass spectrometry data processing

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. 

Bonner R, Burton LL, A new mass spectrometry data processing program, Proc. 43th ASMS Conf., p. 740, 1995. 

Note The abscissa of the TIC or RIC can either be plotted on the time scale, i.e., in units of seconds or minutes, or be labeled with scan numbers. Scan numbers are useful during data processing, while the time scale is better suited for comparison with other chromatography-mass spectrometry data. 

All Bi(OAlk)3 derivatives of n- and z -alcohols are volatile, which permits their purification by distillation, but the yields of the sublimates are low as the processes are accompanied by partial decomposition. A much higher thermal stability is demonstrated by Bi(OBu )3. According to the mass-spectrometry data the first members of the homologous series are dimeric in the gas phase, while Bi(OR% and Bi(0C2H40Me)3 are monomeric [967], However the solid state structure of the latter contains the polymer chains and its solutions in benzene — the dimeric molecules. The NMR spectra indicate the equilibrium in solution of aggregates with different number of chelated ligands [1069]. This obstacle hinders the crystallization of 2-methoxyethoxide from solutions (Table 12.15). 

While those who used the MALDI-TOF MS data had a higher accuracy of positive assignments, this study indicated there are many respondents who are not well versed in the proper use of mass spectrometry data. Respondents can use mass spectra data to confirm sequence assignments within approximately 0.1% accuracy of the measured mass, to estimate the length of a peptide, and to potentially confirm tentative amino acids. The mass spectral data should not be used to estimate the ratios of ions present. The web sites listed in Table II provide a ready resource to aid in this process. 

An alternative to isolation is small-scale synthesis. If possible, structures have been proposed from the mass spectrometry data, one can study the synthetic chemistry and determine at which step of the process the impurity... 

Hastings CA, Norton SM, Roy S. New algorithms for processing and peak detection in liquid chromatogra-phy/mass spectrometry data. Rapid Commun Mass Spectrom 2002 16 (5) 462-7. 

An alternative to isolation is small-scale synthesis. If possible structures have been proposed from the mass spectrometry data, one can study the chemical process and determine at which step of the process the impurity and/or degradant is most likely to be formed. By knowing the chemical process, the feasibility of the proposed structures can be evaluated. Proposed structures can then be synthesized if a reasonable synthesis method is available. It is easier to synthesize and identify an unknown compound if the chemical process works quickly (i.e., one step/straightforward process). The synthesis must be the most efficient route. 

DENDRAL uses a set of rule-based methods to deduce the molecular structure of organic chemical compounds from chemical analysis and mass-spectrometry data. This process includes detecting structural fragments, generating structural formula from these fragments, and verifying it by determining the correlation between... 

Smith, C.A. et al., XCMS Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification, Anal. Chem., 78(3), 779, 2006. 

Increasing reproducibility of available separation techniques and sensitivity and affordability of mass spectrometers, as well as the desire and need to automate the identification process, have caused peptide mass fingerprinting and MS/MS sequencing to gain importance and to become the method of choice for many proteomics laboratories. Several tools are available to assist users in the interpretation of mass spectrometry data. Peptldent (http //www.expasy.org/tools/peptident.html) on the ExPASy server follows the concept of the other tools from the ExPASy proteomics suite, in that it takes into account annotation available in the SWISS-PROT/TrEMBL database, in particular as post-translational modifications and processing are concerned. The user can paste peptide masses (monoisotopic or average) into the Peptldent form, but peptide mass data can also be uploaded from a file on the user s local computer. Supported file formats are .pkm ... 

Smith, C. A., Want, E. J., Tong, G. C., Abagyan, R. Siuzdak, G. (2006). XCMS Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification, Anal. Chem. 78 779-787. 

Lindner, R., Lou, X., Reinstein, J., et al. (2014) Hexicon 2 Automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. J Am Soc Mass Spectrom, 25 (6), 1018-1028. 

Fredriksson M, Petersson P, Jornten-Karlsson M, Axelsson BO, Bylund D. An objective comparison of pre-processing methods for enhancement of liquid chromatography-mass spectrometry data. J Chromatogr A 2007 1172 135—150. 

Fleming CM, et al. Windowed mass selection method A new data processing algorithm for liquid chromatography—mass spectrometry data. J Chromatogr A 1999 849 71-85. 

Jaitly N, et al. Decon2LS An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 2009 10 87. 

Stanstrup J, Gerlich M, Dragsted LO, Neumann S. Metabolite profiling and beyond approaches for the rapid processing and annotation of human blood serum mass spectrometry data. Anal Bioanal Chem. 2013 405 5037-5048. 

Another difficulty associated with conventional mass spectrometry is making quantitative measurements. Determining the rates of gas formation from mass spectrometry data is difficult because for each product either a sensitivity factor must be known or calculated or calibration standards must be measured. For example, from tnethylenenitramine the factors that must be determined for the detection process... 

The luciferin produces a blue oxidation product during its purification process. In the DEAE chromatography of luciferin, this blue compound is eluted before the fractions of luciferin. The fractions of the blue compound were combined and purified by HPLC on a column of Hamilton PRP-1 (7 x 300 mm) using methanol-water (8 2) containing 0.1% ammonium acetate. The purified blue compound showed absorption peaks at 234, 254, 315, 370, 410, 590 (shoulder) and 633 nm. High-resolution FAB mass spectrometry of this compound indicated a molecular formula of C l C Nai m/z 609.2672 (M - Na + 2H)+, and mlz 631.2524 (M + H)+]. These data, together with the HNMR spectral data, indicated the structure of the blue compound to be 8. 

---