msInspect allows you to
process and 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. msInspect is an open source application written in Java.
msInspect is also a platform for rapid development of proteomics
applications. Three applications written using the msInspect platform
have been
the subject of publications:
- msInspect/AMT
is an Accurate Mass and Time workflow for combining LC-MS and LC-MS/MS
peptide data.
- MRMer is a tool
for evaluating MRM ion
candidates and measuring product-ion quantities. Developed in
partnership with Dr. Dan Martin, ISB.
- Qurate
is a tool for visually evaluating quantitation results from
isotopically labeled MS/MS experiments.
The current version of msInspect is 2.3, released January 2010. Release Notes
Having trouble with msInspect? Visit our support site,
which contains an issues list.
If there is an issue with msInspect that is fixed but not yet rolled into an official release, the nightly build will have the fix. Warning: the nightly build may have bugs!
Information
for Developers, including Developer's Guide
Before You Begin
- To conduct the
alignment and regression steps
necessary to create peptide arrays and to use the AMT workflow, 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 Project.
Running msInspect
There are two ways to run
msInspect:
- From the web:
launch msInspect with Java Web Start. This
requires Java
Web Start. We recommend this for first-time or casual users.
- Advantages:
this is very simple, works on all platforms, and will ensure that
you're always working with the latest version.
- Disadvantages:
only the graphical user interface is accessible this way (no
commandline access), though you can access commandline functionality
graphically. You are limited to the default maximum memory size.
- From the JAR
file: download and
run msInspect from a JAR
file. This is the most powerful way to run msInspect, recommended
for serious users.
- Advantages:
you can make changes to parameters such as the amount of memory
allotted to msInspect. You can run commands directly from the
commandline
- Disadvantages:
you will need to
invoke msInspect with a cryptic command: "java -Xmx1024M -jar
viewerApp.jar"
Documentation
- The msInspect User's Guide walks you carefully
through some of the basic functionality of msInspect, especially
viewing runs, finding peptides, creating peptide arrays.
- The msInspect Command Line Manual documents all of
the functionality available from the command line. This document
is automatically generated by msInspect and is also available via the
"--usermanual" command in msInspect.
- The Accurate Mass and Time
and MRM
functionalities within amsInspect are documented separately.
- The
msInspect Developer's Guide
is aimed at
people who want to extend the msInspect platform.
Sample Data
We have some sample data files (small excerpts of
much larger data files) that will give you an idea how the tool works.
The first file is used along with the Sample Feature Set file in the
Tutorial section of the User's Guide. The ICAT sample file is used in
the "Finding Features in Isotopically-Labeled Data" section of the
User's Guide.
Support
Having trouble with msInspect? Visit our support site,
which contains an issues list.
Getting Started (a
brief overview)
A 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.
Development Information
Want to extend or contribute to msInspect, or use
the msInspect platform to create your own applications?
Download the
msInspect Developer's Guide.
Our Code
Documentation is available online.
The
version 2.3 source code is available online. Everything you need to
develop with msInspect is contained in this zip file. The Ant build
file build/build.xml will compile the code.
Read-only access to the msInspect Subversion source code
repository is available. Here's what you need to access the repository:
You can access this repository with the "svn" command in Linux, or with
software like TortoiseSVN
in Windows. This repository will always contain the latest and greatest
msInspect code, meaning that it may be severely broken a good deal of
the time. :) We suggest using the newest released version of msInspect
unless you want to make enhancements to the code.
msInspect includes code from several open source
projects. We would
like to acknowledge them here:
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