Implementation and Evaluation of a Myrimatch Adapter

Student
Dimitri Schachmann

Academic Advisor
Prof. Dr. Knut Reinert, Chris Bielow

Expose

The goal of this thesis is to design, implement and test a TOPP tool in OpenMS method that

1. wraps the id engine myrimatch [1] using mzML as input and idXML as output
2. wraps the id engine inspect [2] using mzML as input and idXML as output
3. compare the performance gain of ConsensusID [3] with current adapters (Mascot, OMSSA, X!Tandem) when including myrimatch and inspect

The adapter should be robust towards missing input files, wrong myrimatch/inspect versions and support the sensible myrimatch/inspect functionality.

Literature

1. Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Journal of proteome research. 2007;6(2):654-61. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2525619&tool=pmcentrez&rendertype=abstract [Accessed March 11, 2012].
2. Tanner S, Shu H, Frank A, et al. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Analytical chemistry. 2005;77(14):4626-39. Available at: http://www.ncbi.nlm.nih.gov/pubmed/16013882 [Accessed October 18, 2011].
3. Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O. Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification. Journal of proteome research. 2011. Available at: http://www.ncbi.nlm.nih.gov/pubmed/21644507 [Accessed June 28, 2011].

Work Plan

1. read literature (1 week)
2. review other adapters in OpenMS (1 week)
3. implement myrimatch/inspect wrapper (4 weeks)
4. benchmark ConsensusID (3 weeks)
5. write up thesis (3 weeks)

Reports

To be filled out by student according to progress on a weekly basis.

Week 1

• Read the literature on MyriMatch and ConsensusID. Will turn to InsPecT as soon as the MyriMatch wrapper is done.
• Looked into the stucture of OpenMS and the wrappers for other search engines.

Week 2

• Begun an implementation of the MyriMatchAdapter. Very basic still.

Week 3+4

• Done with implementing the MyriMatchAdapter. Still some debugging to do.

Tagebuch

• http://page.mi.fu-berlin.de/schachma/thesis/notes.html