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. The program can read instrument data in the following formats:

• Thermo .Raw files
• mzML files (see notes below)
• mzXML files
• mzData files
• .cdf/.mgf combo files

Results are saved both as flat files (.txt) and in an XML file that can be read using the accompanying graphical results browser, MASIC 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.

The application note describing MASIC is: Monroe ME et. al., Comput Biol Chem. 2008 Jun;32(3):215-217. More info is on PubMed

Downloads

Download a .zip file with the installer from: https://github.com/PNNL-Comp-Mass-Spec/MASIC/releases

The release page also includes a .zip file with MASIC_Console.exe

Installation

Double click file MASIC_Installer.exe file to install.
The program shortcut can be found at Start Menu -> Programs -> PAST Toolkit -> MASIC
The MASIC browser shortcut can be found at PAST Toolkit -> MASIC Browser

Console Version

The GUI version of MASIC, file MASIC.exe, includes a command line interface. To see the options, use MASIC.exe /?
See below for more information on the command line arguments.

Alternatively, use program MASIC_Console.exe, which is a command-line only version of MASIC. MASIC_Console.exe can be run on Linux using Mono

Custom SIC Values

You can optionally define custom values to instruct MASIC to create SICs of specific m/z values centered around a certain time point in the input file. You can define the custom values via three methods:

1. Using the Custom SIC Options tab in the GUI
2. Using a tab-delimited text file, which you select in the GUI or via the "CustomMZFile" setting in the "CustomSICValues" section of a MASIC XML parameter file
3. Using the "MZList", "ScanCenterList", and "ScanCommentList" settings in the "CustomSICValues" section of a MASIC XML parameter file

For all three methods, you can define three types of time modes:

• Absolute: absolute scan number
• Relative: relative time ranging from 0 (the first scan) to 1 (the last scan)
• AcquisitionTime: scan acquisition time, aka elution time (in minutes)

When defining custom SIC values, you must provide, at a minimum, the m/z value to search for. If no other values are provided, the default m/z search tolerance will be used (defined on the SIC Options tab in the GUI), and the entire dataset will be searched for the m/z value. You can optionally also define:

1. A custom m/z tolerance to use for each m/z

• If 0, the default SIC tolerance will be used

2. The central scan number or scan acquisition time you want the search to be centered around

• If 0, will be set to the mid-point of the dataset

3. The scan or time tolerance to search forward or backward from the central scan or time

• If 0, will use the default scan or time tolerance

4. A comment to associate with each custom m/z search value

If you use the GUI to define the Custom SIC values, then the column titles shown in the Custom SIC Values table will change based on the Tolerance Type defined.

If you define a tab-delimited text file from which to read the Custom SIC search details, the column headers present in the text file define the search tolerances to use. Files CustomMZList.txt and CustomMZList_AcqTime.txt, which are installed with MASIC, show the proper format for a Custom SIC Values file. At a minimum, the file must have a column titled "MZ" which specifies the custom m/z values to search for. If no other columns are present, a default tolerance is used for the m/z tolerance and the entire file will be searched for each custom m/z file. If you add other columns of data to the file, additional tolerances can be defined. Allowable column names are: MZToleranceDa, ScanCenter, ScanTolerance, and Comment

The data in columns ScanCenter and ScanTolerance can be absolute scan numbers, relative scan numbers, or acquisition time values. The mode to use can be defined in the GUI using the "Tolerance Type" option on the Custom SIC Options tab. Alternatively, if running MASIC from the Command Line, the mode to use must be defined using the "ScanType" setting in section "CustomSICValues" of an XML parameter file ("ScanType" can be "Absolute", "Relative", or "AcquisitionTime").

Instead of using column names ScanCenter and ScanTolerance you can alternatively use the column names ScanTime and TimeTolerance. When these columns are present, then the values in those columns will be treated as AcquisitionTime values, regardless of the global custom SIC Tolerance Type setting defined in the GUI or in the XML parameter file.

Output File Columns

_ScanStats.txt file columns

| Column Name | Description | |----------------------------|----------------------------------| | Dataset | Dataset name | | ScanNumber | Scan number | | ScanTime | Elution time (minutes) | | ScanType | 1 for MS1, 2 for MS2 | | TotalIonIntensity | Total Ion Intensity (TIC) | | BasePeakIntensity | Base Peak Intensity (BPI) | | BasePeakMZ | m/z value of the base peak | | BasePeakSignalToNoiseRatio | S/N of the base peak | | IonCount | Number of ions (after filtering) | | IonCountRaw | Number of ions | | ScanTypeName | HMS, HCD-HMSn, CID-MSn, etc. |

_SICStats.txt file columns

| Column Name | Description | |---------------------------------|-------------------------------------------------------------| | Dataset | Dataset name | | ParentIonIndex | Index | | MZ | Parent ion m/z | | SurveyScanNumber | Precursor scan number | | FragScanNumber | MS2 scan number | | OptimalPeakApexScanNumber | Scan number of the peak apex | | PeakApexOverrideParentIonIndex | Index of the parent ion that this SIC inherits from; -1 if not inherited | | CustomSICPeak | 1 if a peak for a custom m/z search value | | PeakScanStart | SIC peak start scan number | | PeakScanEnd | SIC peak end scan number | | PeakScanMaxIntensity | SIC peak center scan number | | PeakMaxIntensity | Maximum intensity of the SIC peak | | PeakSignalToNoiseRatio | Signal to noise ratio (S/N) | | FWHMInScans | Full width half max, in scans | | PeakArea | Area of the SIC peak | | ParentIonIntensity | Intensity of the parent ion | | PeakBaselineNoiseLevel | Baseline noise level surrounding the peak | | PeakBaselineNoiseStDev | Baseline noise Standard Deviation | | PeakBaselinePointsUsed | Number of points used to determine the baseline noise level | | StatMomentsArea | Area, as computed using statistical moments | | CenterOfMassScan | Central scan number, as determined via the center of mass (from statistical moments) | | PeakStDev | Standard deviation, from statistical moments | | PeakSkew | Skew, from statistical moments | | PeakKSStat | KSStat, from statistical moments | | StatMomentsDataCountUsed | Data points used by statistical moments calculations | | InterferenceScore | Parent ion interference score, measuring the fraction of observed peaks in the parent ion isolation window that are from the precursor |

Reporter Ions

Enable the "Generate Reporter Ion Stats" option to instruct MASIC to look for standard reporter ion masses and to save their observed intensities in file _ReporterIons.txt. Supported reporter ion modes are shown in the following table The integer value corresponds to the number that appears in the MASIC settings file, e.g. <item key="ReporterIonMassMode" value="16" /> for TMT 11

| Integer Value | Name | Description | Ions (m/z values) | |---------------|-------------------------|---------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------| | 1 | iTraq | Original 4-plex iTRAQ | 114.1112, 115.1083, 116.1116, and 117.115