Анализ масс-спектров пептидных фрагментов для идентификации генетически детерминированного полиморфизма белков
Диссертация
Недостатки указанных выше подходов хорошо известны. В базах данных экспрессируемых фрагментов содержится избыточная информация, включая ошибки секвенирования, что усложняет анализ результатов масс-спектрометрического исследования. Анализируя образец, в котором идентифицировано несколько сотен белков, полученные масс-спектры необходимо сопоставлять с накопленными за десятки лет сотнями тысяч… Читать ещё >
Содержание
- ВВЕДЕНИЕ, ЦЕЛЬ И ЗАДАЧИ
- 2. ОБЗОР ЛИТЕРАТУРЫ
- 2. 1. Масс-спектрометрия в протеомике
- 2. 1. 1. Общие принципы
- 2. 1. 2. Протеомный анализ с использованием масс-спектрометрии
- 2. 1. 3. Идентификация белков методом отпечатков пептидных масс
- 2. 1. 4. Идентификация белков методом отпечатков фрагментации пептидов
- 2. 2. Интерпретация результатов масс-спектрометрической идентификации белков
- 2. 2. 1. Определение списка идентифицированных белков
- 2. 2. 2. Идентификация высокогомологичных белков
- 2. 2. 3. Базы данных аминокислотных последовательностей белков
- 2. 3. Масс-спектрометрический анализ продуктов одного гена
- 2. 3. 1. Протеотипирование и популяционная протеомика
- 2. 3. 2. Идентификация микрогетерогенности белков методом «сверху-вниз»
- 2. 3. 3. Идентификация генетически-детерминированного полиморфизма белков методом «снизу-вверх»
- 2. 3. 4. Базы данных полиморфизмов белков и генов
- 2. 3. 5. Репозитории масс-спектрометрических данных
- 2. 1. Масс-спектрометрия в протеомике
- 3. 1. Материалы
- 3. 1. 1. Масс-спектрометрические данные для белков микросомальной фракции печени человека
- 3. 1. 2. Контрольный набор масс-спектров «Aurum Dataset»
- 3. 1. 3. Масс-спектрометрические данные протеомного репозитория PRIDE
- 3. 1. 4. Базы данных аминокислотных последовательностей белков человека
- 3. 1. 5. Данные о возможных полиморфизмах белков человека
- 3. 2. Методы
- 3. 2. 1. Веб-сервер идентификации белков по масс-спектрам
- 3. 2. 2. Пакетная обработка масс-спектров методом отпечатков пептидных масс
- 3. 2. 3. Пакетная обработка тандемных масс-спектров
- 3. 2. 4. Одномерное протеомное картирование
- 3. 2. 5. Программная реализация итеративного алгоритма идентификации ОАП
- 3. 2. 6. Валидация алгоритма идентификации ОАП
- 4. 1. Увеличение степени покрытия аминокислотных последовательностей идентифицированными пептидами
- 4. 1. 1. Идентификация белков в срезах геля
- 4. 1. 2. Одномерные протеомные карты и их свойства
- 4. 1. 3. Выявление высокогомологичных белков надсемейства цитохромов Р450 за счет увеличения степени покрытия аминокислотных последовательностей идентифицированными пептидами
- 4. 2. Идентификация ОАП в белках надсемейства цитохромов Р
- 4. 3. Алгоритм идентификации ОАП
- 4. 3. 1. Итеративная схема обработки тандемных масс-спектров
- 4. 3. 2. Чувствительность и специфичность алгоритма идентификации ОАП
- 4. 4. Применение итеративного алгоритма для выявления ОАП в масс-спектрометрических данных протеомного репозитория PRIDE
- 4. 4. 1. Исходные данные, используемые для выявления ОАП
- 4. 4. 2. Идентификация пептидов и белков с использованием масс-спектрометрических данных, загруженных из репозитория PRIDE
- 4. 4. 3. Идентификация одноаминокислотных полиморфизмов
- 4. 5. Анализ идентифицированных ОАП
- 4. 5. 1. Анализ ОАП-содержащих пептидов
- 4. 5. 2. Связь выявленных ОАП с заболеваниями человека
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