Monocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.
Project Folders:
Monocle - The class library project containing the core algorithm.
Monocle.CLI - The console application project.
Monocle.UI - The windows application project.
Monocle.Tests - The unit testing project.
Authors: Ramin Rad, Devin Schweppe
Copyright © 2019-2020 Gygi Lab and the above authors.
For licensing (commercial and non-commercial) of Monocle (including Monocle, Monocle.CLI, Monocle.UI, and Monocle.Tests), please contact the authors.
For the purposes of reading RAW data files: The RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
Download the zip file from the latest release above, extract and navigate to it's contents. Run the Monocle.CLI.exe file with the -f option to specify the input file and the -t option to specify the output type. The output file will be written in the same directory as the input file.
The following output types are supported:
- csv
- mzxml
- mzml
Example:
Monocle.CLI.exe -f x00123.raw -t csv
Builds for the monocle library and the monocle cli app use the dotnet core command line.
# Run Tests in Monocle.Tests
dotnet test
# Debug build
dotnet build
# Build Release exe in Monocle.CLI
# Use -r for the runtime that applies to you
dotnet publish -c Release -r win10-x64
-f, --File Required. Input file for monoisotopic peak correction
-n, --NumOfScans The number of scans to average, default: +/- 6
-a, --AveragingVector Choose to average scans "Before" the parent scan, "After" or "Both" (default).
-c, --ChargeDetection Toggle charge detection, default: false | F
-z, --ChargeRange Range for Charge Detection, if enabled. default: 2:6
-u, --ChargesForUnknown For low-res scans, output multiple precursors with these charges. default: 2:3
-w, --ForceCharges Output multiple precursors with charges set by -u even if charge is known. default: false
-m, --MsLevel Select the MS level at which monoisotopic m/z will be adjusted.
-i, --UseMostIntense Re-assign precursor m/z to the most intense peak in the isolation window.
-q, --QuietRun Do not display file progress in console.
-t, --OutputFileType Choose to output an mzXML "mzxml" or CSV file "csv".
-o, --OutputFilePath File to write. Include directory, filename, and extension
--help Display this help screen.
--version Display version information.