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msInspect Release Notes

Version 2.2, September 2009

This version debuts a greatly-expanded Qurate, including tools for automatically (rather than manually) evaluating the quality of quantitative events.  It also adds some more graphical utilities for developers.
  • New Features
    • Qurate now has a robust workflow for locating the most extreme proteins in an experiment and the most extreme quantitative events for those proteins, to cut down evaluation workload.  It also automatically assesses each quantitative event and provides heuristic guidance for curation.
  • Under the Hood
    • There are a few new graphics utilities in the platform, including support for layers on charts that are sensitive to mouse selection (as showcased in Qurate).
    • msInspect version 2.2 depends on JFreeChart 1.0.13, up from 1.0.6 in msInspect 2.1.

Version 2.1, March 2009

This version is released in support of our Technical Note in JPR: A software platform for rapidly creating computational tools for mass spectrometry-based proteomics.  The main focus is on making the msInspect platform into an effective set of tools for building proteomics applications.  Please see the msInspect Developer's Guide to learn how to use the platform.

  • New Features
    • Expanded platform tools, including new tools for creating pie charts, generating HTML snippets, effectively displaying charts, and other goodies.  Better platform documentation.
    • The Qurate application (discussed in our JPR paper) for visually evaluating isotopically labeled quantitation results, is now included with the platform.

Version 2.0, October 2008

Why 2.0, rather than 1.3? We're considering this a major revision because we're adding two major new pieces of functionality: MRMer and a probability model for msInspect/AMT.

Also, we've done some major reorganization of the code, to make it very easy to develop prototype proteomics applications on our platform. If you're working with msInspect source code and having trouble with the new code organization, please contact the support forum.

  • New Features

    • A Windows installer and executable now make it easier for Windows users to use msInspect
    • AMT:
      • A statistical model is implemented for AMT matches to infer individual match probability
      • We've added tools for integrating AMT match data with MS/MS database search results
      • AMT databases can now record MS1 retention times, rather than MS/MS identification retention times, for more accurate retention time matching
    • The MRMer tool for MRM analysis is now part of the standard msInspect release
    • msInspect now supports the APML v2.0 standard file format for LC-MS peptide features

  • Usability Improvements

    • We've added a Windows executable and installer
    • --usermanual command dynamically generates and displays an HTML-formatted user manual, for all of msInspect or for a single command
    • All errors are automatically tracked, and error information is logged to a file that can be sent to the msInspect support forum for assistance
    • --log argument for all commands generates a verbose logfile that can be useful for debugging issues
    • Extensive improvements to "interactive" mode (--interactive command) for running commands. "Interactive" mode is now extremely helpful for finding appropriate argument values

  • Under the Hood

    • Major reorganization of code into "toolbox" (more generally useful code) and "msinspect" (msInspect-specific functionality) packages.  We've made it extremely easy to build proteomics applications on the msInspect platform without taking up the entire codebase.
    • We've moved into a new source code repository,  so you'll notice lower revision numbers than before

Version 1.2.1, September 2007

  • New Features

    • Full Accurate Mass and Time workflow (create AMT databases and match MS1 peptides to those databases in order to increase peptide identifications). This work is related to our article in JPR, A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data.
    • MS1 feature-finding mass accuracy improvements
    • Peptide feature file conversion between PepXML, SpecArray, and msInspect formats
    • Extract per-fraction pepXML files from a multi-fraction pepXML file
    • Create "consensus" feature sets from a peptide array, containing only features found in multiple runs
    • CPAS file-browsing UI, which allows you to connect to an instance of CPAS, browse the project and folder structure, and download data files. Compatible with CPAS 2.1
    • Usability improvements: "command files" and "interactive mode"