Protein Mixture Inference as Hitting Set Variants and Linear Algebra Problems
Doktorsavhandling, 2013

This work is dedicated to the problems of protein inference and quantification in bottom-up proteomics, and, in particular, in shotgun proteomics. We adopt a rather classical approach of representing inference problem as a set cover, where proteins are understood as sets of their observations: peptides' masses or sequences. However, we seek concise enumeration of all possible mixtures rather than some optimal mixture. Such enumeration gives insight on how likely every protein is to be in the correct mixture. In general, the corresponding Set Cover instances, are not very hard unless one admits, that there were experimental errors. Therefore we state that the hardest part is to first remove all possible errors. The corresponding computational problem's formulation is provided. We proceed with studying its complexity and performance in practice. Protein quantification problem is modeled in terms of linear systems. We advocate use of shared peptides in the data. It is known that these data makes analysis more difficult and error-prone. We study how bad can be error propagation, if one uses shared peptides. We conclude with a method for adjusting incorrect observations, given that their number is considerably low.

Union Editing

Shotgun proteomics

Parameterized complexity

Protein Inference

Shared Peptides

Set Cover

Hypergraph

Hitting Set

Fixed Parameter Tractable

Protein Quan- ti

Star Editing

ED-salen, D&IT, Chalmers
Opponent: Prof. Henning Fernau, Department of Computer Science, University of Trier, Germany

Författare

Leonid Molokov

Chalmers, Data- och informationsteknik, Datavetenskap

Fixed-parameter tractability of error correction in graphical linear systems

7th International Workshop on Algorithms and Computation WALCOM 2013, Lecture Notes in Computer Science,; Vol. 7748(2013)p. 245-256

Paper i proceeding

Application of Combinatorial Methods to Protein Identification in Peptide Mass Fingerprinting

KDIR 2010 - International Conference on Knowledge Discovery and Information Retrieval, Valencia, Spain,; (2010)p. 307-313

Paper i proceeding

The union of minimal hitting sets: parameterized combinatorial bounds and counting

Journal of Discrete Algorithms,; Vol. 7(2009)p. 391-401

Artikel i vetenskaplig tidskrift

Error propagation in sparse linear systems with peptide-protein incidence matrices

Lecture Notes in Computer Science,; Vol. 7292(2012)p. 72-83

Paper i proceeding

Parameterized reductions and algorithms for a graph editing problem that generalizes vertex cover

Theoretical Computer Science,; Vol. 452(2012)p. 39-46

Artikel i vetenskaplig tidskrift

Styrkeområden

Informations- och kommunikationsteknik

Livsvetenskaper och teknik

Fundament

Grundläggande vetenskaper

Ämneskategorier

Bioinformatik (beräkningsbiologi)

Datavetenskap (datalogi)

ISBN

978-91-7385-833-5

Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie

ED-salen, D&IT, Chalmers

Opponent: Prof. Henning Fernau, Department of Computer Science, University of Trier, Germany