application GC/MS P ro d u c t i v i t y To o l s : D o S c a n Enhance Productivity by Reprocessing Raw Data with DoScan Introduction What is DoScan? A modern analytical laboratory handles an immense quantity of sample information. In order for the laboratory to be efficient, that information must flow from sample preparation through data acquisition and reduction and ultimately into reporting and into the company’s electronic ocean. Any individual area in the process can become a bottleneck inhibiting the efficient flow of information and causing a decrease in productivity. In medium to high sample volume GC/MS analyses, situations frequently occur in which the analyst is required to reprocess a complete or partial sequence or batch of samples. Fortunately, there are numerous productivity-enhancing tools contained within Agilent Technologies' MSD Productivity ChemStation software. These tools, which help the operator to optimize the flow and to reprocess information, include: DoList, Qedit, and DoScan. DoScan is one of the MSD Productivity ChemStation tools designed to increase laboratory productivity. It is an interactive reprocessing utility that facilitates the flow of information for the analyst. DoScan differs from the other ChemStation productivity tools in that it allows the analyst to select various mass spectral scans or chromatographic peaks for searching in a commercial mass-spectral library database or in a user-created library. The DoScan function is available in both the Enhanced and Environmental data analysis modes of the MSD Productivity ChemStation software. DoList is a tool for reprocessing a single sample data file or a batch of data files in a manner similar to that used in the original processing (publication no. 5968-4366E). Qedit, which is a quantitation-results editor, allows the user to visually review and correct integration and retention-time identification of compounds and recalculate results and update the existing quantitation database (calibration data). DoScan is especially useful when a number of unknown peaks are found in a chromatogram that has been acquired in a scan mode of operation. Rather than selecting the peaks one-by-one and library-searching and printing the results individually, DoScan allows the analyst to select at once all the peaks that require further identification and to then print a library report showing the best matches for all the selected peaks. As a result, in long chromatographic runs in which there are many unidentified peaks, DoScan can produce significant savings in analyst time. Productivity Tools: DoScan How Does DoScan Work? DoScan is a data-reduction function found under Tools in the Data Analysis menu as illustrated in Figure 1. Once DoScan is activated, a Report dialogue box appears. See Figure 2. In the Enhanced version of the ChemStation, the user can select one of two choices. The first choice in the Select a Report Option dialog box allows the analyst to generate a ChemStation Library Search Report that shows the unknown scan compared with the library spectrum. In addition, the five major mass spectral ions are extracted, information that is useful in determining the purity of the unknown peak. At the bottom of the page, the three best matches from each library are shown along with the corresponding quality value. This Library Search Report provides the information necessary to identify an unknown. The second choice in this dialog box allows the analyst to select a user-generated macro for the library searching and report style. In the Environmental Data Analysis mode, an additional report style, Report LSC, is available. See Figure 3. The LSC (Library Search Compound) provides a report of non-target compounds or of tentatively identified compounds. Figure 3. The Select a Report Option dialog box from the Environmental Data Analysis mode; this mode of operation provides the Library Search Compound report style. Figure 1. Activating the DoScan Productivity Tools in Data Analysis under the Tools menu item (in the Enhanced version of ChemStation). Figure 2. The Select a Report Option dialog box in the Enhanced Data Analysis mode; two report options are available. 2 Productivity Tools: DoScan Selecting Peaks for the Library Search After the Select a Report Option dialog box is closed, the mouse cursor is activated in the Annotation mode. Clicking both mouse buttons simultaneously selects a given peak in this mode. When both mouse buttons are clicked, the scan closest to that mouse pointer in the total ion chromatogram (TIC) is selected for the library search and the peak of interest is designated with a small plus sign (+). The zoom functions of the MSD Productivity ChemStation software that utilize the left and right mouse buttons are active during this operation. Hence the analyst can select points on the up-slope and down-slope of the peak to determine sample purity and to verify the match quality of the searched spectra. Once all the peaks have been selected, the DoScan list is activated. A report is generated by clicking on the Tools menu item entitled Process Scan List as illustrated in Figure 4. See Figure 5 on the following page. Figure 4. After selecting all the peaks for the library search, the DoScan list is activated by Process Scan List under the Tools menu item. DoScan is only one of the many productivity tools provided with the MSD Productivity ChemStation software that allow the laboratory analyst to be more efficient. When utilized effectively, DoScan can save considerable time and lead to increased productivity. 3 Productivity Tools: DoScan Figure 5. An example of a Library Search Report for one compound; the report includes actual spectrum (top), best three library hits from two different libraries (bottom), and the five select-ion chromatograms for the five largest abundance’s (right). Windows NT® is a U.S. registered trademark of Microsoft Corporation. Windows® is a U.S. registered trademark of Microsoft Corporation. Agilent Technologies shall not be liable for errors contained herein or for incidental or consequential damages in connection with the furnishing, performance or use of this material. Information, descriptions and specifications in this publication are subject to change without notice. Copyright © 1999 Agilent Technologies Company All rights reserved. Reproduction and adaptation is prohibited. Printed in the U.S.A. December 1999 (23) 5968-4365E