https://github.com/gygilab/Monocle

Monocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.
https://github.com/gygilab/Monocle

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Monocle is a tool for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments.

• Host: GitHub
• URL: https://github.com/gygilab/Monocle
• Owner: gygilab
• Created: 2019-08-20T21:22:06.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2024-08-10T18:28:32.000Z (3 months ago)
• Last Synced: 2024-08-10T19:56:58.720Z (3 months ago)
• Language: C#
• Homepage:
• Size: 11.6 MB
• Stars: 8
• Watchers: 5
• Forks: 6
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-proteomics - Monocle - C# - for monoisotopic peak and accurate precursor m/z detection in shotgun proteomics experiments. - [paper](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00563) (4. Assorted pipeline Tools / Table of Contents)

README

        
# 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.