Download The 8 Queens Problem (and how to solve it)

Software Project
MassAnalyst
Roeland Luitwieler
Marnix Kammer
April 24, 2006
Overview
Introduction
System requirements
Our solution: Spectre
Progress so far
Conclusion
2
Introduction
Project initiator
Scientific background
The need for software tools
3
Project initiator
Dr. ir. Bas van Breukelen
Department of Biomolecular Mass
Spectrometry
Utrecht University!
 WENT building

Expert in:
Bioinformatics
 Proteomics

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Scientific background:
Proteomics
Our body consists of cells
Cell functionality and structure is offered by
proteins
Proteomics
Main research areas:
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Identification of proteins
Interaction of proteins
Comparison of protein levels
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Protein identification
How to identify proteins?
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Identity defined by their structure
Protein structure
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Protein: sequence of peptides
Peptide: sequence of amino acids
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20 common types
Consist of different atoms – have different masses
Too small to see… but not to weigh
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Mass Spectrometry!
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Mass Spectrometry (MS)
Technique using a mass spectrometer
Input: sample of peptides

Proteins have been split chemically
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Provides a.o. more accuracy, efficiency
Most head / tail subsequences are present
Output: mass spectrum
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Frequencies of particles of certain masses
Full peptide sequence can be derived
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Mass Spectrometry (MS)
How does it work?
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Ionize particles
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Accelerate them in an
electric field
Deflect them in a
magnetic field
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Now particles have an
electrical charge
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 details
 Output: a sequence of MS spectra
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Mass Spectrometry (MS)
Improvements for better analysis (2)

Use “recursive” mass spectrometry
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Called MS/MS (or MS2 or tandem MS)
Take part of the sample that produces a peak
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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 mzXML
 A database is searched on MS/MS spectra
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Input: raw MS data
Output: pepXML: peptide information

Tools are used to e.g. display the data
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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
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Filtering, “warping”, peak detection, etc.
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Bioinformatics:
existing tools
Tools exist, but…
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Lots of different tools to do different things
Functionality not always as desired
They also lack functionality
Not easily extendable
Example: Pep3D
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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
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Use in open community
Open source
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Loading data
mzXML: raw spectrometry data
MS spectra
 Embedded 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
spectra
Workspace: a collection of samples and
settings
Sample: internal data structure for one
sample
GUI: the user interface
Processor: the main link between parts of
the program
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The structure of
Spectre
GUI
1
1
Processor
*
Workspace
4
Graph
*
Sample
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Systematic approach
to the problem
Phased development

Three versions
Lots of diagrams

Application of courses MSO, PM
HCI team and data layer team
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Later on: data visualization team
Extreme Programming
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Progress so far
First version will be due in week 18
Functionality:
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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 23
Warping
 Peak detection / analysis
 Export of calculated data
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Version 3 – week 27
Ratio calculation
 Modification of samples

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After completion of the project
Web site
Open source
further maintaining
 extendable

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Conclusion
Spectre: a modular and extendable
program
A combination of many different
requirements
Phased addition of features
Any questions?
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The data structure
Sample
1
MzTable
SampleParser
SampleWriter
*
MzNode
MzParser
PepParser
…
…
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