Data processing peak detection

Despite these advancements in chromatographic data processing, peak detection and integration algorithms were crude, the user interface was cumbersome, and there was very little flexibility in the types of reports that these systems could generate. 

Separation of components occurs as the analytes and mobile phase are pumped through the column. Eventually, each component elutes from the column as a narrow band or peak on the recorder. Detection of the eluting components is important, and this can be either selective or universal, depending upon the detector used. Tlte response of the detector to each component is displayed on a chart recorder or computer screen and is known as a chromatogram. To collect, store, and analyze chromatograms, computers, integrators, and other data processing equipment are frequently used. 

After generation, the metabolites must be extracted and isolated. A variety of sample pretreatment methods can be applied, such as protein precipitation, liquid extraction, liquid-liquid extraction (LLE), solid-phase extraction (SPE), and microdialysis. Cleanup prior to LC-MS analysis is essential to reduce endogenous interferences and small peaks at every m/z in the mass spectra. The cleanup step also facilitates the data processing and peak detection in the chromatogram. 

A variety of tools are available for the detection and characterization of the metabolites. Unless advanced data-acquisition strategies (Ch. 10.4.4) are applied, at least two LC-MS analyses are required. The first injection is performed in full-spectrum LC-MS mode, preferable using an MS system with improved full-spectrum sensitivity, such as (linear) ion trap and time-of-flight (TOP) instruments. The analysis of a blank extract next to real samples greatly facilitates peak detection and avoids further work on endogenous peaks. The data are processed to find the relevant /w/z-values of potential metabolites. These /w/z-values are used as precursor ion m/z in a subsequent (time-scheduled) product-ion LC-MS-MS analysis. Again, instruments with improved full-spectrum sensitivity, such as ion-traps, quadrapole-linear ion trap hybrids (Q-LIT), or quadrapole-TOF hybrids, are favourable. 

After analysis, target compounds (those compounds that the analysis is aiming to detect) are recorded by the data processing facilities of the mass spectrometer (Figure 41.3). The correct location of target peaks in a gas chromatogram is verified by the use of target-compound databases,... 

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. 

C) Processing of the MS data and protein identification. A flexible and interactive tool has been developed to automatically perform peak detection and calibration on all spectra. The positions on the sample plate are converted to apparent molecular mass (Mr) and pi values. The PMF data of all spectra, together with the calculated pi and Mr and other user defined parameters (such as mass tolerance, considered chemical modifications, species, etc.), are automatically submitted to Peptldent for identification... 

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