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  • Boston

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Achievements

Achievement: QuickdrawAchievement: Pair Extraordinairex2Achievement: Pull Sharkx3Achievement: Galaxy BrainAchievement: Arctic Code Vault ContributorAchievement: Starstruck
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mobiusklein/README.md

I'm a bioinformatician who works with mass spectrometry data. My PhD was dedicated to developing computational methods for glycomics and glycoproteomics, finding integrated-omics strategies to dig deeper into complex biological samples. My professional work now involves using that knowledge to analyze immunopeptidomics data to help develop better cancer vaccines. :email: Email me if you want to discuss MS data processing techniques, glycoinformatics, or antigenomics

🔬 Active Projects

I'm actively working on these projects. They get updated frequently. Please contact me if you want to know more about them or if you find them useful!

  • glycresoft: A glycan and glycopeptide LC-MS/MS search engine
  • ms_deisotope: A mass spectrometry library and executable for data access, signal processing, deisotoping, and charge state deconvolution suite. Actively working to deconvolute raw ion mobility data supporting Waters Cyclic IMS and Bruker TIMS-TOF data.
  • glypy: A glycoinformatics library for reading, writing, and manipulating glycans, as well as access to glycoinformatics resources around the web.

Supporting Libraries

These libraries receive updates as needed, but their purpose is to serve my other active projects. If they look useful to you, please let me know.

  • psims: Write HUPO PSI-MS mzML and mzIdentML XML formats.
  • brainpy: A library to generate coarse theoretical isotopic patterns.
  • ms_peak_picker: A low level library for signal processing of raw mass spectra
  • glycopeptidepy: A library to model glycopeptides and how they fragment. An extension to glypy.

Popular repositories

  1. cython_pyinstaller_example cython_pyinstaller_example Public

    A simple example repository describing the process of building a PyInstaller executable for a Cython-compiled program

    Cython 44 11

  2. ms_deisotope ms_deisotope Public

    A library for deisotoping and charge state deconvolution of complex mass spectra

    Python 31 14

  3. glypy glypy Public

    Glycan Analysis and Glycoinformatics Library for Python

    Python 26 14

  4. ms_peak_picker ms_peak_picker Public

    A small library to provide peak picking for software processing mass spectrometry data

    Cython 20 9

  5. brainpy brainpy Public

    A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

    Python 19 10

  6. psims psims Public

    A declarative API for writing XML documents for HUPO PSI-MS mzML and mzIdentML

    Python 19 9