Software Project MassAnalyst

Roeland Luitwieler

Marnix KammerApril 24, 2006

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Overview

Introduction

System requirements

Our solution: SpectreProgress so far

Conclusion

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Introduction

Project initiator

Scientific background

The need for software tools

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Project initiator

Dr. ir. Bas van BreukelenDepartment of Biomolecular Mass SpectrometryUtrecht University!WENT building

Expert in:BioinformaticsProteomics

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Scientific background: Proteomics

Our body consists of cellsCell functionality and structure is offered by proteins

ProteomicsMain research areas: Identification of proteins Interaction of proteins Comparison of protein levels

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Protein identification

How to identify proteins? Identity defined by their structure

Protein structure Protein: sequence of peptides Peptide: sequence of amino acids

20 common types Consist of different atoms – have different masses

Too small to see… but not to weigh Mass Spectrometry!

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Mass Spectrometry (MS)

Technique using a mass spectrometer

Input: sample of peptides Proteins have been split chemically

Provides a.o. more accuracy, efficiency Most head / tail subsequences are present

Output: mass spectrum Frequencies of particles of certain masses Full peptide sequence can be derived

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Mass Spectrometry (MS)

How does it work? Ionize particles

Now particles have an electrical charge

Accelerate them in an electric field

Deflect them in a magnetic field

Deflection depends on mass (F = m a)

Measure how far they have been deflected

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Mass Spectrometry (MS)Improvements for better analysis (1)Use chromatography

Spreads input over time: more detailsOutput: a sequence of MS spectra

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Mass Spectrometry (MS)Improvements for better analysis (2) Use “recursive” mass spectrometry

Called MS/MS (or MS2 or tandem MS) Take part of the sample that produces a peak

Usually concerns one certain peptide Output: MS spectra with related MS/MS spectra

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Mass Spectrometry (MS)

Improvements for better analysis (3)Use bioinformatics

All output is translated to mzXMLA database is searched on MS/MS spectra

Input: raw MS data Output: pepXML: peptide information

Tools are used to e.g. display the data

Lots of redundant / boring work is taken care of!

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Bioinformatics:what can be done?

Remember the Proteomics research areas: Identification of proteins Interaction of proteins Comparison of protein levels

Most research: differ one aspect at a time

Requires interactive display of data Zooming, “stacking”, cross sections, etc.

But not just display of data Filtering, “warping”, peak detection, etc.

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Bioinformatics:existing tools

Tools exist, but… Lots of different tools to do different things Functionality not always as desired They also lack functionality Not easily extendable

Example: Pep3D Nice visualization, but Only one sample at a time, only a single view

Solution: develop new software

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System requirements

Load raw spectrometry data

Visualize the data

Manipulate and analyze the data interactively

Export data

Extendibility Use in open community Open source

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Loading data

mzXML: raw spectrometry dataMS spectraEmbedded MS/MS spectra

pepXML: database of matches with peptides

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Visualizing the data

List of loaded samples

MS spectrum

Cross sections of the MS spectrum

MS/MS spectra

Peptide information

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Manipulating and analyzing the data

Stacking: toggle samples on/off

Warping

Zooming

Peak detection

More analysis, like ratio calculation

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Export data

Lists of peak pairs

Modified PepXML (i.e. with ratios)

Images of spectra

Modified samples

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Our solution: Spectre

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Opening a workspace

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Loading a workspace

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After the workspace is loaded

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Working in normal mode

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Zoom on selection mode

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After zooming in

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Zoom on click mode

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After zooming in

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The structure of Spectre

Graph: MS spectra, cross sections, MS/MS spectraWorkspace: a collection of samples and settingsSample: internal data structure for one sampleGUI: the user interfaceProcessor: the main link between parts of the program

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The structure of Spectre

Processor

GUI

Workspace

Sample

Graph

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Systematic approachto the problem

Phased developmentThree versions

Lots of diagramsApplication of courses MSO, PM

HCI team and data layer teamLater on: data visualization team

Extreme Programming

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Progress so far

First version will be due in week 18

Functionality: Loading raw data Visualization and user interface Basic interaction with zooming etc. Complete internal data structures Export of images

Missing link between mzXML and pepXML!

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Further planning

Version 2 – week 23WarpingPeak detection / analysisExport of calculated data

Version 3 – week 27Ratio calculationModification of samples

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After completion of the project

Web site

Open source further maintainingextendable

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Conclusion

Spectre: a modular and extendable programA combination of many different requirementsPhased addition of features

Any questions?

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The data structure

MzTable

Sample

MzNode*

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SampleParser SampleWriter

MzParser PepParser … …