Mass analysis data-dependent

Depending on the objectives of the analysis, the mass spectrometer will be operated in various modes of data acquisition such as MS, tandem MS or MS/MS, selected ion monitoring (SIM), multiple reaction monitoring (MRM), fiill-scan or limited mass range, data dependent, and so forth. SIM/MRM conditions will improve the detection limits, while data-dependent MS/MS acquisitions will worsen them. The data acquisition/storage speed and the number of averaged spectrum are all factors that will ultimately affect the detection limits. 

MS/MS Duty Cycle Typical MS/MS analysis is a serial process, relying on the selection of precursors (peptides) in MS mode, followed by high-energy fragmentation in MS/MS. This process is termed data dependent acquisition (DDA). The duty cycle for the completion of MS and MS/MS cycles (the time necessary for MS/MS spectrum acquisition) is of primary importance. When the separation performance is viewed from the mass spectrometry perspective, the peak capacity can be characterized by the number of MS/MS scans, yielding successful... 

By employing a laser for the photoionization (not to be confused with laser desorption/ ionization, where a laser is irradiating a surface, see Section 2.1.21) both sensitivity and selectivity are considerably enhanced. In 1970 the first mass spectrometric analysis of laser photoionized molecular species, namely H2, was performed [54]. Two years later selective two-step photoionization was used to ionize mbidium [55]. Multiphoton ionization mass spectrometry (MPI-MS) was demonstrated in the late 1970s [56—58]. The combination of tunable lasers and MS into a multidimensional analysis tool proved to be a very useful way to investigate excitation and dissociation processes, as well as to obtain mass spectrometric data [59-62]. Because of the pulsed nature of most MPI sources TOF analyzers are preferred, but in combination with continuous wave lasers quadrupole analyzers have been utilized [63]. MPI is performed on species already in the gas phase. The analyte delivery system depends on the application and can be, for example, a GC interface, thermal evaporation from a surface, secondary neutrals from a particle impact event (see Section 2.1.18), or molecular beams that are introduced through a spray interface. There is a multitude of different source geometries. 

When a particular component eluting at a certain retention volume is to be estimated, this approach can be outlined as follows. Since SEC is extremely reproducible, the peak shape, peak width and peak height are dependent on the amount of the species in the sample volume injected, sample volume and retention time. From these factors the SEC peaks can be simulated or elution pattern of any species within the separation range can be plotted as a function of mass vs. retention volume. The analysis data supplies the concentration of this particular species over two or more 0.5 ml intervals. A match-up computer program has to be developed so that it can pick up the peak shape and concentration based on 3 or 4 data points at known Intervals. 

The LTQ-FT mass spectrometer was introduced in late 2003 and, as expected, the main application discussed in the literature is for the analysis of proteins and peptides (Johnson et al., 2004 Syka et al., 2004). A recent book chapter (van der Greef et al., 2004) and a review article (Brown et al., 2005) discussed the application of the LTQ-FT to metabolomics. FTMS applications to dmg metabolism are still very new and dmg discovery research laboratories which have recently purchased the instmment are still in the process of developing and validating methods and approaches. A recent publication describes the depth and flexibility of the experimental setup utilizing accurate mass data-dependent exclusion MS" measurements with a LTQ-FT (Tozuka et al., 2005). We have reported several integrated approaches for determination of metabolic stability, characterization of metabolites and metabolic... 

Lim, H. K., Chen, J., Sensenhauser, C., Cook, K., and Subrahmanyam, V. (2007). Metabolite identification by data-dependent accurate mass spectrometric analysis at resolving power of 60,000 in external calibration mode using an LTQ/Orbitrap. Rapid Commun. Mass Spectrom. 21 1821-1832. 

Data-dependent software programs allow real-time decisions to be made during an analysis. This approach features a preestablished threshold for the detection of a peak during full-scan mass spectrometry and MS/MS scan modes. If a peak of interest is detected in real-time, then the mass spectrometer is switched from full-scan mode to another scan mode to obtain more information from the same analysis. For example, the system may be automatically switched to the production mode during the analysis of a chromatographic peak to obtain substructural information. Thus, more detailed information is obtained in fewer analyses. This powerful... 

As with PDA detection and the construction of UV libraries, computerized data systems are used for data collection and processing with mass spectral detection. Unlike UV spectra, however, mass spectra are much less dependent on experimental conditions. Thus, it is possible to purchase commercial libraries of mass spectra for spectral matching. Mass spectral data systems range from systems that record the spectra and produce conventional relative abundance bar charts for subsequent analysis to those... 

The same tryptic digest protein sample was analyzed by capillary LC/MS/MS using an ion trap mass spectrometer followed by a database search with SEQUEST. Fig. 4 illustrates the components of an ion trap mass spectrometer. The highly automated data-dependent MS/MS analysis provided excellent sequence coverage for 11 tryptic peptides related to AlAT in a single LC/MS run. A tryptic peptide that corresponds to the AlAT sequence SVLGQLGITK observed at retention time (r,) 30.5 min. was observed in the spectrum. The LC/MS data also provided sequence information on unmatched MALDI peaks. 

The rapid structure identification of metabolites is a powerful complement to previously described quantitative approaches. The utility of an automated metabolite identification approach, using LC/MS/MS with an ion trap mass spectrometer has been demon-strated.f In this study, MS" analysis is automated to provide maximum structural information in combination with predictive strategies for biotransformation. Automated data-dependent scan functions are used to generate full scan, MS/MS, and MS" mass spectra of... 

Tiller et al. demonstrated an analytical strategy with on-line LC/UV/MS and LC/MS/MS to rapidly obtain structural information for leachables from a drug-delivery device. Similar to proteomics-based applications, the analysis strategy makes use of data-dependent analysis, wherein the mass spectrometer first obtains molecular ions using full-scan techniques, and makes real-time decisions about MS/MS product-ion spectra that must be obtained. In this way, molecular weight and substructural information are both obtained for many components during a single HPLC run. 

Figure 37-18 Sequence polymorphism analysis by mass spectrometry. The underlined base is the polymorphic site in the template (T or C). Single-stranded template is primed and extended in the presence of three dNTPs and one ddNTP, producing fragments of different mass depending on the sequence.The boxed A in this example indicates the incorporated terminator adenine base.The mass of terminated products is precisely measured by MALDI-TOF mass spectrometric data (relative intensity versus m/z).

The result obtained from the film theory is that the mass transfer coefficient is directly proportional to the diffusion coefficient. However, the experimental mass transfer data available in the literature [6], for gas-liquid interfaces, indicate that the mass transfer coefficient should rather be proportional with the square root of the diffusion coefficient. Therefore, in many situations the film theory doesn t give a sufficient picture of the mass transfer processes at the interfaces. Furthermore, the mass transfer coefficient dependencies upon variables like fluid viscosity and velocity are not well understood. These dependencies are thus often lumped into the correlations for the film thickness, 1. The film theory is inaccurate for most physical systems, but it is still a simple and useful method that is widely used calculating the interfacial mass transfer fluxes. It is also very useful for analysis of mass transfer with chemical reaction, as the physical mechanisms involved are very complex and the more sophisticated theories do not provide significantly better estimates of the fluxes. Even for the description of many multicomponent systems, the simplicity of the model can be an important advantage. 

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