MIMA V 1.0. MS IMS Mapper. Peak Identification in Ion mobility Spectrometry

Transcription

1 MIMA V 1.0 MS IMS Mapper Peak Identification in Ion mobility Spectrometry

2 I. What is MIMA? MIMA is a software package for mapping mass-spectrometric (MS) data to corresponding ion-mobility spectrometer (IMS) derived chromatograms. Its focus is the automation of the MS to IMS and IMS to IMS peak assignment. II. Method summary Ion-mobility spectrometry is an analytical detection method for volatile substances and is often coupled with mass spectrometry. Peak assignment of MS and IMS data is a frequent operation for identification of indistinct peaks in complex IMS samples. A drawback of a manual comparison of MS and IMS measurements is the high expenditure of time and the requirement of at least two parallel running software tools to compare both chromatograms. MIMA automates this process by generating an IMS Layer using both the corresponding OpenChrom - preprocessed MS data and an IMS database. The layer contains the analytes from the MS measurement and the corresponding coordinates within the IMS-chromatogram. It can be automatically superposed on IMS chromatograms using the IMS analysis software VisualNow. III. Where is MIMA developed? MIMA was developed at Max Planck Institute Informatik, in cooperation with the KIST Europe, Saarbrücken. IV. MIMA input formats First, for the generation of an analyte list using OpenChrom, a MS data file corresponding to the IMS file is needed Second, for the generation of an IMS Layer an IMS Database is necessary V. MIMA output formats The MIMA software package creates an analyte list as well as an IMS Layer in Microsoft Excel format (*.xls). VI. Languages The MIMA software supports three languages: English, German and French.

3 VII. Workflow MS - IMS: Assuming we would be interested in identifying the peak, highlighted by an arrow (see Fig. 1), in the IMS chromatogram by crosschecking a corresponding gas chromatograph-mass selective detector (GC-MSD) measurement we would perform the following steps: Fig. 1 Peak of interest. Configuration of Open Chrom: 1. Install OpenChrom according to the instructions given on the website (tested for version 0.8.0). 2. Install the following plugins via Plug-Ins -> OpenChrom Marketplace: -Agilent MSD Import Converter -NIST-DB Connector 3. Use the OpenChrom preferences dialogue to set the correct NIST database (nistms$.exe) via Window-> Preferences->Identifier-> Nist Identifier (Set NIST path/ Set number of Targets =10) and run the OpenChrom Demo. 4. Before you can use the batch functionality of the OpenChrom open source software to generate a report file (*.txt) from a *.MS file (example) the following two steps have to be performed:

4 First set a new OpenChrom project in the Project explorer (window->select view- >project explorer) by right-clicking in the explorer window and choose New -> Project -> MS Projects-> Analysis Project and name it (Fig.2) Fig. 2 Start a new analysis project and name it Second, open a new batch process job in by right-click in the Project explorer window and choose New -> Other -> MS Projects-> Analysis Project and save it in your new generated analysis project folder (Fig.3). Fig. 3 Start a new batch process job and select your new analysis project as saving folder. 5. Then edit the batch process in the following way (Fig. 4): Select the input file type *.MS with Input files-> Add *. Add the Process Entries categories Peak Detector, Peak Integrator and Peak identifier with the corresponding plugins Peak Detector #1, Peak Integrator #1 and NIST Peak Identifier to the process entries list.

5 Select in the report supplier OpenChrom.txt as file format and define an output folder. Fig. 4 Edit the batch process. 6. Run the batch process in Batch Process Job Editor- > Run the batch process to create a report file from your MS data file (Fig.5). Fig. 5 Run the batch process.

6 Configuration of MIMA: 1. Start MIMA by double clicking. Generate a new project in File -> Create Process-> MS- IMS Mapping and enter a process name (Fig.6). Fig. 6 MIMA user interface 2. Drag and drop the OpenChrom created report file *.txt to the field A (Fig.6). A B D C Fig. 7 Process Setup 3. Select the directory of the IMS reference database file using the Open button in B (Fig.7). 4. Select the result folder using the Open button in C (Fig.7). 5. Select one of the following processing options in D (Fig.7): All Analytes: Consider all Analyt-Proposals for a GCMS-Peak in the IMS DB

7 Best Matching Analyte: Select the first Analyte that occurs in the IMS DB Best Analyte: Only search for the best Analyte candidate for each GCMS peak in the IMS DB 6. Start the calculation by pressing the Start Processing button in D. 7. Load your chromatogram, which you want to analyze in the IMS software VisualNow. Build an IMS-Set. Load the MIMA created layer file (Fig. 8). Fig. 8 Peak of interest annotated with layer.

8 VIII. Workflow IMS IMS Layer Annotation 1) Open Program: Double click on MIMA-1.0.jar And Create a Layer Annotation process. Fig. 9 MIMA user interface 2) Fill the required information: B A D C E Fig. 10 Process Setup. A. Select the IMS DB file using the OpenButten. B. Select the Layer files in your file-browser and drag them into the corresponding field. C. Select the result folder using the Open button. D. Select a Processing Option:

9 i. Euclidean Distance : Select the analyte of minimal Euclidean distance to the target peak. ii. Solely Overlapping: Select the analyte of maximal overlap to the target peak. iii. Overlap->Eucl. Diststance: Apply as ii, for those target peaks without overlapping peaks or no decision is possible, the Euclidean distance is applied. iv. Eucl. Distance -> Overlap: Apply as i, for those target peaks without single closest peak, the overlap is applied. 3) Start the calculation by Pressing the Process button E