Biological MS Data and Software Distribution Center at PNNL

MASIC (MS/MS Automated Selected Ion Chromatogram generator)

MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. The SICs are generated using the LC-MS data, then each SIC is processed using a peak finding algorithm to characterize the chromatographic peaks, providing peak statistics including elution time of the peak apex, peak area, and peak signal/noise.

MASIC can read Finnigan .Raw files, mzXML files, mzData files or .cdf/.mgf combo files. Results are outputted both as flat files (.txt) and in an XML file that can be read using the accompanying graphical results browser. The browser provides a fast, graphical method for browsing the SICs identified by MASIC, allowing the user to sort and filter the SIC list as desired. MASIC has been in routine use in the PRISM pipeline since 2004 and has been used to process over 40,000 datasets. MASIC has also been updated to provide basic support for MRM datasets.

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Software Details
Version v2.5.3050 Requirements Microsoft .NET Framework 3.5
Date Updated May 8, 2008 File Size (Software Tool) 2.2 MB (ZIP)
Registration Required No File size (Source Code) 5.4 MB (ZIP)
Developers Matthew Monroe
Comments See the complete Revision History for a history of changes

 

MASIC Screenshots

MASIC GUI

MASIC Graphical user interface

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The MASIC user interface allows you to customize the processing options for generating selected ion chromatograms, exporting raw data, etc.

 

MASIC Results Browser

MASIC Results Browser

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The MASIC Results Browser displays a list of the Selected Ion Chromatograms (SICs) generated by the software. You can sort the list and view individual SICs. The green dots indicate the spectra in which this m/z was chosen for MS/MS analysis.

 

Acknowledgment

All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.