Кертес-Фаркаш Аттила Вычислительные методы для аннотирования данных тандемной масс-спектрометрии

brief description

Кертес-Фаркаш Аттила Вычислительные методы для аннотирования данных тандемной масс-спектрометрии
ОГЛАВЛЕНИЕ ДИССЕРТАЦИИ
доктор наук Кертес-Фаркаш Аттила
Contents

1 Introduction

1.1 The relevance of research

1.2 Importance of work

1.3 Novelty and summary of the Author's main results

1.4 Publications

2 Computational Mass Spectrometry

2.1 Spectrum data generation

2.2 Peptide spectrum scoring

2.2.1 Spectrum discretization

2.2.2 Spectrum filtering and preprocessing

2.2.3 Score functions

2.3 Discriminative property

2.4 Score calibration

2.4.1 Analytical approaches

2.4.2 Linear approaches

2.4.3 Exact approaches

2.4.4 Heuristic approaches

2.5 P-value calibration

2.6 Comparison of score functions

2.7 Universality property

2.8 Learning new score functions

3 Evaluation of database searching results

3.1 False discovery rate

3.2 FDR control with target-decoy approach

3.2.1 Q-values

3.3 FDR control with P-values

3.4 Unbiasedness property of score functions

4 Error-tolerant search

4.1 Missed and unexpected cleavages

4.2 Modifications

5 Large search space

6 Main developed methods

6.1 Learning of new score functions

6.1.1 The BoltzMatch method

6.1.2 The Diversifying Regularization method

6.1.3 The Slider method

6.2 Statistical methods which improve the power of annotation methods

6.2.1 The Tailor method

6.2.2 Bias evaluation in spectrum annotation

6.2.3 The Cascaded search method

6.2.4 The Mix-Max method

6.3 Modification searching

6.3.1 The PTMSearch method

6.3.2 The PTMTreeSearch method

6.4 Spectrum filtering methods

6.4.1 The Precursor mass dependent filtering method

6.4.2 The Chemical rule-based filtering method

6.5 The Crux toolkit

6.6 Review papers

6.6.1 Overview on database-searching approach

6.6.2 Review on spectrum data filtering methods

7 Conclusions

8 List of abbreviations and conventions

9 Declarations of author contribution