msInspect allows you to view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration. We also implement a full Accurate Mass and Time (AMT) workflow for combining LC-MS and LC-MS/MS peptides. msInspect is an open source application written in Java.
Before You Begin
- To run msInspect from the web, you must have Java Web Start installed. If you already have Java Web Start installed, you can enter http://proteomics.fhcrc.org/download/tools/remoteApps.html directly into the Location box in the Java Web Start Application Manager.
- To conduct the alignment and registration steps necessary to create peptide arrays, you must have R installed and on the path. R is available from the R Project for Statistical Computing website.
- To generate mzXML files from native MS acquisition files, try one of the converters from the Sashimi Website.
- For maximum performance, we recommend JRockit JVM (for Windows). You might consider installing BEA JRockit.
Launching msInspectLaunch msInspect with Java Web Start.
(version 1.2.1, June 2007. Release Notes)
You can also download and run msInspect from a JAR file. This allows you to make changes to parameters such as the amount of memory allotted to msInspect.
Download the msInspect User's Guide.
We have a sample data file (a small excerpt of a much larger data file) that will give you an idea how the tool works. It is used along with the Sample Feature Set file in the Tutorial section of the User's Guide.
You can also visit our Command Line Help page on this website.
Getting StartedA file open dialog should appear when you launch the viewer. You can also choose Open from the File menu. msInspect will open any mzXML file containing MS1 data; however, msInspect has been designed for high-resolution LC ESI-TOF MS1 data so it may not perform as well with an mzXML file from another type of MS (e.g., MALDI).When you open a file for the first time, msInspect writes an .inspect file in the same directory as the original mzXML file to make subsequent opening faster. This can be time consuming so we recommend you do it on a machine with a fast connection to the disk where the original mzXML file is stored.
After the image is generated, it will appear in the main Image Pane of the msInspect window. The X axis is scan number, and the Y axis is m/z value. Intensity is represented by the darkness of the spot at any point.
Click an area in the Image Pane to display a zoomed in view in the Detail Pane to the right. Peptide features detected by msInspect are marked with Xs (mono-isotopic peak) and ovals (all peaks grouped together for that feature).
The bottom panel, or Chart Pane, displays m/z spectra and elution profiles. The m/z spectrum corresponds to the scan marked by the vertical red line in the Detail Pane. If you choose to display the elution profile, the Detail Pane displays a horizontal red line marking the m/z value for the profile.
Please see the User's Guide for more details about msInspect's functionality.
Support
Visit our support site, which contains an issues list.
Development Information
Want to extend or contribute to msInspect? Download the Download the msInspect Developer's Guide.
Our Code Documentation is available online. Please note: all classes and methods in these Javadocs are subject to change without notice. At this point there are no msInspect APIs that are guaranteed to be stable. All "stable" APIs are documented in the msInspect Developer's Guide.
The version 1.2.1 source code is available online. Everything you need to develop with msInspect is contained in this zip file. The Ant build file build.xml will compile the code.
msInspect includes code from several open source projects. We would like to acknowledge them here:
Release Notes, msInspect 1.2.1
- 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"
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