Refactoring Efforts for the IBG Mass Spec Database

• Refactoring the Mass Spec Database

XML Interface to Annotations

• OverView
• Use Cases

• Gearing Up
• Deliverables
• Work currently in progress

Overview:

• The IBG Mass Spec Database allows for the insertion and storage of mass spectra.

• A model for annotation of Mass Spec data
  • Harman, Dennis; Angulo, David; Drew, Kevin; Schilling, Alex. Proceedings of the Midwest Software Engineering Conference/DePaul CTI Research Symposium. Chicago, IL. April 29 2006. Poster, Abstract
  • Current version of Database Schema for annotations: annotate_model_updated.gif
  • SQL scripts for creating annotations database tables: sqlScripts_2.txt
  • Current version of XML Schema for annotations:peakAnnotations1_1.xsd

• Implemention of the annotation model.
  • Dennis Harman and David Sigfredo Angulo, "Annotation of Mass Spectrum Data", submitted as a poster to 2007 DEPAUL CTI RESEARCH SYMPOSIUM (CTIRS) Saturday May 5th, 2007, MSAnnotations07_DennisHarman_1.3.doc

Project requirements are based on the following use cases:

GENERAL USE CASES:

• User selects a spectrum to annotate and requests the system to download the spectrum, along with any existing annotations.
• The system extracts the information from the database and assembles it into XML file.
• The system downloads the spectrum, which is presented to the user as downloadable file(s).
• User loads the downloaded file into the IBG Desktop for data visualization and annotation editing.
• The Desktop generates an edited XML file.
• User requests the system to upload the annotated file.
• The system uploads the file and writes it back into the database.

SPECIFIC ANNOTATION SCENARIOS:

• A user should be able to annotate the mass peak of a MS1 spectrum,
  e.g., indicating a mass peak presenting a peptide of interest.
• A user should be able to annotate the mass peak of an interpreted peptide MS/MS fragmentation spectrum,
  e.g., b3, a2, y7, etc.
• A user should be able to indicate the charge state of a mass peak,
  e.g., singly charged as +1, doubly charged as +2, triply charged as +3. etc.
• A user should be able to indicate that a mass peak value represents one or multiple neutral losses,
  e.g., -H2O, -NH3, -CH3SOH, etc.
• A user should be able to indicate that a mass peak in the low-mass region of an MS/MS spectrum represents an immonium ion,
  e.g., mass peaks representing immonium ions arising from histone or proline could be labelled as immonium ion with the single-letter-codes for the parent amino acids, i.e., H and P, respectively.
• A user should be able to annotate a mass peak as an internal cleavage fragment type,
  e.g., a mass peak representing an internal cleavage could be annotated by naming it internal cleavage and showing the amino acid sequence found in the fragment.
• A user should be able to annotate the mass peakS of PTM experiments,
  e.g., the mass peaks of phosphorylated and unphosphorylated forms of a peptide of interest could be annotated as +PO3 and -PO3, respectively;
  e.g., TO DO: FINISH PTM USE CASES
• TO DO: METABOLITE USE CASES

Gearing up:

• Setting up a local copy of IBG-MSP database (refer to the setup procedure under "Resources" on the Mass Spec Database project page).

• Getting an understanding of the application's API by reading the Javadocs.
  • Note in your local installation, you need to execute "ant javadoc", in order for ant to create the API's pages.
  • The destination directory will be dist/docs/api.

• The front end of the IBG-MSP is a Web application built on the struts framework - here's a link to get an understanding of struts "Jakarta Struts 1.2 Tutorial" by Marty Hall

• Understanding fundamentals of mass spectrometry by reading background material.
  • Refer to references listed on the Reading List page, specifically those under the Mass Spectrometry Readings.

• Download the IBG DeskTop, and experiment with the application using a simple DTA file.

Deliverables (more or less prioritized):

Currently in progress:

• Integrating annotations tables into the database located on histone.

• CTIRS-07 Poster

• Refactoring Efforts:
  • Implemention of code using the java.sql package that accesses and queries the database according to mass spectrum specified by the user.
  • structures the annotations data as XML file, and returns it to user as an XML document
  • Implemention of code in the the IBG-Desktop that uses the DTA and XML annotations files and allows the user to edit peak
  • Implemention of servlet code that processes an HTTP request (in the form of an annotations XML file), parses out the data points, and stores it in the database

Relevant time points:

• April 25 (Wed) Deadline for the camera ready version of CTIRS-07 abstracts
• May 5 (Sat) Day of the CTIRS-07 Conference
• June 11 - 15, 2007 - Finals Week, end of Spring quarter

-- DennisHarman - 21 April 2007