mass spectrometry In silico peptide characterization tool (msInspect)

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract msInspect is a suite of software and algorithms for viewing and processing data from liquid chromatography-mass spectrometry (LC-MS) measurements.

It is also a platform for proteomics application development.

msInspect allows you to process and view mass spectrometry (MS1) data in an mzXML file [mzXML is an XML (eXtensible Markup Language) based common file format for proteomics mass spectrometric data].

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.

Three (3) applications written using the 'msInspect platform' is as follows:

1) msInspect/AMT - msInspect/AMT is an Accurate Mass and Time (AMT) workflow for combining LC-MS and LC-MS/MS peptide data.

It can be used for:

The algorithms that support this analysis workflow will Not be discussed in detail here.

For details on the algorithms used, please see May D, Fitzgibbon M, Liu Y, Holzman T, Eng J, Whiteaker J, Paulovich A, McIntosh M. - A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data, Journal of Proteome Research 2007.

2) MRMer - MRMer is a tool for evaluating Multiple Reaction Monitoring (MRM) ion candidates and measuring product-ion quantities.

MRMer was developed in partnership with Dr. Dan Martin of the Institute for Systems Biology (ISB).

MRMer allows you to view and analyze MRM data stored in an mzXML file.

MRMer reads an mzXML file and infers precursor-ion/product-ion relationships.

It displays elution curves of the product ions and allows the user to select or deselect them as candidates for MRM-based assays. It also displays the elution curve of the precursor ions when MS1 scans are present in the mzXML file. MRMer's calculations can be output to a tab-delimited file.

MRMer can also read a specialized tab-delimited file that defines heavy and light ion relationships in SILAC or AQUA experiments.

When this file is present, MRMer calculates and displays the light-to- heavy ratio of the elution AUCs (areas under the elution curves).

The calculation of AUCs is driven by a pluggable 'signal processing' module. This module is called an "ElutionCurveStrategy". Version 0.97 of MRMer supplies one such strategy called the "BasicElutionCurveStrategy".

A Java programmer can create other, more sophisticated strategies. MRMer is an open source application written in Java.

3) Qurate - Qurate is an open-source, Java-based graphical application for visual curation of quantitative data from isotopically-labeled Liquid Chromatography Mass Spectrometry (LC-MS) experiments.

It can help identify quantitative ratios that are incorrect or based on insufficient spectral data and remove those ratios from your dataset.

Qurate takes as input a set of 'search results' (in pepXML format, with optional ProtXML support); including quantitative ratios computed by the XPress or Q3 algorithm, along with their originating mzXML files that encode the raw LC-MS spectral data.

Using Qurate, you can identify quantitated proteins and peptides of interest, and visually curate the associated quantitative events using several different visualizations.

Qurate is distributed as part of the msInspect Platform. msInspect New Features released in Version 2.1 --

1) Expanded platform tools, including new tools for creating pie charts, generating HTML snippets, effectively displaying charts, etc. Better platform documentation.

2) The Qurate application for visually evaluating isotopically labeled quantitation results, is now included with the platform.

Note: The manufacturer's software platform(s) make use of ISB tools, the Global Proteome Machine's ‘X! Tandem’ project - (see G6G Abstract Number 20081), and the R statistical programming language.

System Requirements

Contact manufacturer.


Manufacturer Web Site msInspect

Price Contact manufacturer.

G6G Abstract Number 20406

G6G Manufacturer Number 104036