Monocle

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.

How to use the command-line application

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

How to Build

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

Monocle.CLI Option Information:

-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.