Data-dependent scanning

Triolo, A., Altamura, M., Dimoulas, T., Guidi, A., Lecci, A., and Tramontana, M. (2005). In vivo metabolite detection and identification in drug discovery via LC-MS/MS with data-dependent scanning and postacquisition data mining. J. Mass Spectrom. 40 1572-1582. 

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... 

There have been signihcant advances to harvest the power of the mass spectrometry-based analysis technique. The ability to perform real-time scanning experiments with real-hme automated dynamic feedback has become an essenhal component of qualitahve analysis, such as biotransformahon or proteomics applicahons. Most commercial mass spectrometry software packages provide the ability to perform data-dependent scanning procedures. Metabolic prohling and proteomics generate large quanhties of data that must be quickly and efficiently interpreted and hltered such that the data can be quickly reported in a way that will support rapid decisions. 

Data dependent scanning is a MS technique that utilizes algorithms to automatically make real-time decisions to control the acquisition mode of the mass spectrometer. The data system executes the next scan type based on previously collected data. -Eor example, an ESI mass spectrometer can be programmed to implement the following experiment. 

The application of an Orbitrap platform was also described for this purpose. In this case, one can use the excellent full scan sensitivity of the high-resolution accurate mass measurement in both the survey and data-dependent scan modes in order to identify the reactive intermediates and then provide data for their structure assignment [23], A labeled form of GSH 2 1 ratio of 5mM glutathione and I3( V5N Gly glutathione was used. The high mass accuracy in the survey scan can be used to detect the GSH adduct. The method was successfully applied for the detection and characterization of GSH conjugates of acetaminophen, tienilic acid, clozapine, ticlo-pidine, and mifepristone. 

LC/MS/MS Analysis The samples (75 pL) are loaded onto an Agilent Zorbax RX-C8 column (4.6 mm x 250 mm, 5 pm, Wilmington, DE). The flow rate is set at 1 mL/min with a 1 5 split to the mass spectrometer ion source and a waste container, respectively. The mobile phase consists of solvent A (5 mM ammonium acetate in water-acetonitrile-acetic acid, 95 5 0.05, v/v/v) and solvent B (5mM ammonium acetate in acetonitrile-water-acetic acid, 95 5 0.05, v/v/v). The HPLC runs are programmed by a linear increase from 0% to 80% of solvent B during a 30 min period. The mass spectra are recorded in full scan and data-dependent scans of MS" (n = 2, 3, or 4). The MS" spectra... 

In the Scan Event 2, select Analyzer as Ion Thap for MS/MS, Mass Range and Scan Rate as Normal, and select Centroid option for Data type. Check the box next to Dependent scan, and then click the Settings button to open the Data Dependent Settings dialog box that allows us to set parameters for performing data-dependent scans. 

Check the Enabled box in the Dynamic Exclusion page of the Data Dependent Settings dialog box to select parameters to prevent for a subsequent data-dependent scan after it has already triggered a data-dependent scan. This way, dynamic exclusion prevents an abundant peptide ion with a broad elution profile from being continually selected for MS/MS and allows the ion trap to collect MS/MS spectra on other, less intense ions that would otherwise not be examined. The typical settings include Repeat count of 2, Repeat duration of 30 s, Exclusion list size of 50 and Exclusion duration of 180 s. 

Chck the Settings button to open the Data Dependent Settings dialog box that allows you to set parameters for performing a data-dependent scans. 

Solid-phase extraction and liquid chromatography-tandem mass spectrometry are invaluable techniques for the determination of benzodiazepines and metabolites in biological matrices. The reason for using tandem mass spectrometry is to increase limits of detection without the need for chemical derivatization. Here we describe a technique for the detection of 26 benzodiazepines and metabolites at a detection limit of approximately 1-2 ng/mL in blood and 1-5 ng/mL in urine when screened using a data-dependent scan method. 

Liquid chromatography (LC)/ThermoFisher Scientific LTQ Ion Trap Mass Spectrometer or equivalent capable of tandem mass spectrometry and data-dependent scanning. 

Song, H., Hsu, P.P., Ladenson, J. and Turk, J. (2007) Algorithm for processing raw mass spectrometric data to identify and quantitate complex lipid molecular species in mixtures by data-dependent scanning and fragment ion database searching. J. Am. Soc. Mass Spectrom. 18, 1848-1858. 

Figure 9.23. An example of a data-dependent scanning during an LC separation of a myoglobin tryptic digest...

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