The Multiplierz Proteomics Library
multiplierz is a Python software library and associated GUI desktop environment for managing proteomic mass spectrometry workflows and data analysis. Using the mzAPI interface to native instrument data formats, multiplierz is provides a complete toolset for a variety of methods for peptide identification, quantitation, and experimental reporting.
See the wiki for installation instructions and documentation or at the end of this document for installation instructions to have limited functionality on Linux distributions.
Multiplierz is written for and in Python, a mature and user-friendly language that is becoming a standard for scientific data analysis, and is fully open-source. This allows researchers with programming experience full freedom in customizing and improving the multiplierz library for individual, novel use cases. We expect multiplierz capabilities to grow alongside the rapid developments in the field of computational proteomics.
Typical proteomic bioinformtics workflows use tools such as ProteoWizard to first convert native instrument data into a text-based XML format such as mzML or mzXML; for high-throughput experiments, this entails substantial demands in terms of data processing, storage, and organization. Instead, multiplierz offers fully transparent access to native instrument data through mzAPI, a standardized interface to Thermo, AB Sciex, and Agilent machine data formats, as well as the universal mzML format.
A key step in any proteomic workflow is peptide/protein identification, a sophisticated algorithmic problem solved by applications such as Mascot, Comet, and X! Tandem. To support routine bioinformatic workflows it is necessary to automate the operation of these programs, so multiplierz offers rich, programmatic access to the applications mentioned, with full support for the wide array of parameters requested by each, so that searches can be customized and initiated through elegant Python code.
Note: GUI Interface was released using release v2.2.1 and does not incorporate changes from v2.2.2
Not all biologists are computer scientists, so multiplierz provides a fully-graphical interface to most of its capabilities, including management of MGF and FASTA files, protein coverage visualization, and database search coordination. The mzDesktop GUI application can be found at our Sourceforge page.
Chromatographic Feature Detection, Quantitation Analysis, Intact Protein Charge Deconvolution, and more...
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04/09/2024: Minor Update (2.2.2) Python3 compatibility; pythonnet for .D (Agilent) files; patches/instructions for install and .raw format access.
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12/04/2019: Minor Update (2.2.1) Python 3 compatibility fixes
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12/04/2019: Major Update (2.2.0) adds Linux compatibility and Bruker data format access!
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08/22/2017: The paper on multiplierz's 2.0 release has been published in Proteomics.
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08/01/2017: mzStudio, an interactive proteomics data browser built using multiplierz, has been published in Proteomes.
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05/22/2017: Major Update (2.0.0) The 2.0 release edition of multiplierz is pending publication! We will update here as features are added, bugs are fixed, etc.
Please cite if you use multiplierz in an academic publication:
Alexander, William M., et al. "multiplierz v2.0: a Python-based ecosystem for shared access and analysis of native mass spectrometry data." Proteomics (2017).
Questions related to use and modification of the multiplierz library should be referred to W. Max Alexander at williamM_alexander@dfci.harvard.edu.
Note: Also confirmed to run in a Docker Container (run on CentOS 7/8)and Windows Subsystem for Linux (WSL)
$ python -m pip install --upgrade pip
$ sudo apt-get update
$ sudo apt-get install -y wget git
$ wget -q https://packages.microsoft.com/config/ubuntu/18.04/packages-microsoft-prod.deb
$ sudo dpkg -i packages-microsoft-prod.deb
$ rm packages-microsoft-prod.deb
$ sudo apt-get install -y apt-transport-https clang libglib2.0-dev nuget
$ sudo apt-get update
$ sudo apt-get install -y aspnetcore-runtime-5.0
$ sudo apt-get install -y dotnet-sdk-5.0
$ sudo apt-get install -y dotnet-runtime-5.0
$ sudo apt-get install -y gnupg ca-certificates
$ sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
$ echo "deb https://download.mono-project.com/repo/ubuntu stable-bionic main" | sudo tee /etc/apt/sources.list.d/mono-official-stable.list
$ sudo apt-get update
$ sudo apt-get install -y mono-devel
$ pip3 install multiplierz
$ python -c "from multiplierz.mzAPI.management import registerInterfaces; registerInterfaces()"
The last line may produce a warning that module 'ctypes' has no attribute 'windll'; this should be safe to ignore for use with XCalibur .RAW files.