Course Information

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science

Timetable

each even Friday 8:00–9:50 C02/211

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 30 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Timetable

Fri 8:00–9:50 C02/211

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 30 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Timetable

Fri 8:00–9:50 C02/211

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Timetable

Fri 8:00–9:50 C02/211

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Timetable

Fri 10:00–11:50 Kontaktujte učitele

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives

Lecture, directed mainly to students of biological programs, gives a brief introduction into mass spectrometry (MS) of proteins including selected related techniques and examples of MS applications. The main goal of the lecture is understanding of principles and possibilities of mass spectrometry in protein characterization. Student should obtain an overview of MS applicability in molecular biological and medical research and other fields.

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Assessment methods

lecture, colloquium

Language of instruction

Czech

Further comments (probably available only in Czech)

Study Materials
The course is taught annually.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites (in Czech)

Základní znalosti z biochemie a molekulární biologie

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives (in Czech)

Přednáška podává studentům, především biologických oborů, stručný úvod do metod využívajících hmotnostní spektrometrii k identifikaci proteinů a jejich modifikací včetně vybraných alternativních technik a praktických příkladů.

Syllabus (in Czech)

• 1. Hmotnostní spektrometrie Princip metody, vymezení možností metody, stručný přehled instrumentace a ionizačních technik (MALDI-TOF MS, ESI-IT MS, FTMS, hybridní systémy). 2. Příprava vzorku (RNDr. Hana Konečná) Obecné zásady přípravy vzorku pro MS analýzu. Strategie zpracování proteinových vzorků (volba vhodného souboru technik vzhledem k požadovanému výsledku experimentu). 3. Základní metody identifikace proteinů Peptide mapping, MS/MS ion search, identifikace proteinů s neznámou sekvencí (de-novo sequencing), výhody a limitace jednotlivých metod, základní proteomické přístupy (bottom-up, top-down), podobnost proteinů. 4. Kvantifikace Metody relativní a absolutní kvantifikace v hmotnostní spektrometrii (hmotnostní značky, specifické značky typu iTRAQ). 5. Určování modifikací proteinů Přehled druhů modifikací (post-translační modifikace, chemické modifikace), identifikace mutací. Fosfoproteiny příprava vzorku pro analýzu fosforylovaných proteinů a jejich detekce, určení místa fosforylace. Glykoproteiny separace a detekce glykoproteinů, analýza sacharidových residuí. 6. Proteinové čipy (RNDr. Šárka Pospíšilová, PhD) Druhy proteinových čipů, jejich příprava, detekce a kvantifikace proteinů vazaných na čipech. 7. Proteomické aplikace Hmotnostní spektrometrie a diagnostika nemocí (identifikace biomarkrů, protein profiling), praktické příklady řešené na půdě PřF.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.
The course is taught: every week.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites (in Czech)

Základní znalosti z biochemie a molekulární biologie

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives (in Czech)

Přednáška podává studentům, především biologických oborů, stručný úvod do metod využívajících hmotnostní spektrometrii k identifikaci proteinů a jejich modifikací včetně vybraných alternativních technik a praktických příkladů.

Syllabus (in Czech)

• 1. Hmotnostní spektrometrie Princip metody, vymezení možností metody, stručný přehled instrumentace a ionizačních technik (MALDI-TOF MS, ESI-IT MS, FTMS, hybridní systémy). 2. Příprava vzorku (RNDr. Hana Konečná) Obecné zásady přípravy vzorku pro MS analýzu. Strategie zpracování proteinových vzorků (volba vhodného souboru technik vzhledem k požadovanému výsledku experimentu). 3. Základní metody identifikace proteinů Peptide mapping, MS/MS ion search, identifikace proteinů s neznámou sekvencí (de-novo sequencing), výhody a limitace jednotlivých metod, základní proteomické přístupy (bottom-up, top-down), podobnost proteinů. 4. Kvantifikace Metody relativní a absolutní kvantifikace v hmotnostní spektrometrii (hmotnostní značky, specifické značky typu iTRAQ). 5. Určování modifikací proteinů Přehled druhů modifikací (post-translační modifikace, chemické modifikace), identifikace mutací. Fosfoproteiny příprava vzorku pro analýzu fosforylovaných proteinů a jejich detekce, určení místa fosforylace. Glykoproteiny separace a detekce glykoproteinů, analýza sacharidových residuí. 6. Proteinové čipy (RNDr. Šárka Pospíšilová, PhD) Druhy proteinových čipů, jejich příprava, detekce a kvantifikace proteinů vazaných na čipech. 7. Proteomické aplikace Hmotnostní spektrometrie a diagnostika nemocí (identifikace biomarkrů, protein profiling), praktické příklady řešené na půdě PřF.

Language of instruction

Czech

Further Comments

Study Materials
The course is taught annually.
The course is taught: every week.

Bi7050 Charakterizace proteinů hmotnostní spektrometrií

Extent and Intensity

1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites (in Czech)

Základní znalosti z biochemie a molekulární biologie

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives (in Czech)

Přednáška podává studentům, především biologických oborů, stručný úvod do metod využívajících hmotnostní spektrometrii k identifikaci proteinů a jejich modifikací včetně vybraných alternativních technik a praktických příkladů.

Syllabus (in Czech)

• 1. Hmotnostní spektrometrie Princip metody, vymezení možností metody, stručný přehled instrumentace a ionizačních technik (MALDI-TOF MS, ESI-IT MS, FTMS, hybridní systémy). 2. Příprava vzorku (RNDr. Hana Konečná) Obecné zásady přípravy vzorku pro MS analýzu. Strategie zpracování proteinových vzorků (volba vhodného souboru technik vzhledem k požadovanému výsledku experimentu). 3. Základní metody identifikace proteinů Peptide mapping, MS/MS ion search, identifikace proteinů s neznámou sekvencí (de-novo sequencing), výhody a limitace jednotlivých metod, základní proteomické přístupy (bottom-up, top-down), podobnost proteinů. 4. Kvantifikace Metody relativní a absolutní kvantifikace v hmotnostní spektrometrii (hmotnostní značky, specifické značky typu iTRAQ). 5. Určování modifikací proteinů Přehled druhů modifikací (post-translační modifikace, chemické modifikace), identifikace mutací. Fosfoproteiny příprava vzorku pro analýzu fosforylovaných proteinů a jejich detekce, určení místa fosforylace. Glykoproteiny separace a detekce glykoproteinů, analýza sacharidových residuí. 6. Proteinové čipy (RNDr. Šárka Pospíšilová, PhD) Druhy proteinových čipů, jejich příprava, detekce a kvantifikace proteinů vazaných na čipech. 7. Proteomické aplikace Hmotnostní spektrometrie a diagnostika nemocí (identifikace biomarkrů, protein profiling), praktické příklady řešené na půdě PřF.

Language of instruction

Czech

Further Comments

The course is taught annually.
The course is taught: every week.

Bi7050 Physiology of Cellular Systems

The course is not taught in Autumn 2002

Extent and Intensity

2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).

Teacher(s)

prof. RNDr. Jiřina Hofmanová, CSc. (lecturer), doc. RNDr. Martin Vácha, Ph.D. (deputy)
prof. RNDr. Alois Kozubík, CSc. (lecturer), doc. RNDr. Martin Vácha, Ph.D. (deputy)

Guaranteed by

prof. RNDr. Jiřina Hofmanová, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 18 student(s).
Current registration and enrolment status: enrolled: 0/18, only registered: 0/18, only registered with preference (fields directly associated with the programme): 0/18

fields of study / plans the course is directly associated with

• Ecotoxicology (programme PřF, M-BI)
• Molecular Biology and Genetics (programme PřF, M-BI)
• Molecular Biology and Genetics (programme PřF, N-BI)
• General Biology (programme PřF, M-BI, specialization Physiology of Animals)
• General Biology (programme PřF, N-BI, specialization Physiology of Animals)

Language of instruction

Czech

Further Comments

The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.

Bi7050 Protein characterisation using mass spectrometry

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites

Basic knowledge of biochemistry and molecular biology

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives

At the end of the course students should be able to: understand and explain the basic principles of mass spectrometry; describe MS instrumentation currently used in proteomics understand to basics of interpretation of MS and MS/MS data explain to principles of protein identification and their posttranslational modifications by mass spectrometry explain principles of MS quantification methods describe present possibilities of mass spectrometry in proteomics propose application of appropriate mass spectometric techniques for different types of biological and biomedical experiments

Syllabus

• 1. Mass spectrometry (MS)
• Method principles, method possibilities, overview of MS instrumentation and ionization techniques (MALDI-MS, ESI-IT MS, FTMS, hybrid systems).
• 2. Sample preparation and separation (RNDr. Hana Konečná)
• General rules for sample preparation before MS analysis. Strategies for processing of protein samples (selection of appropriate techniques in consideration of purpose of experiment).
• 3. Basic methods of protein identification
• Peptide mapping, MS/MS ion search, identification of proteins with unknown sequence(de-novo sequencing), basic proteomic approaches (bottom-up, top-down), protein homology.
• 4. Quantification
• Methods of relative and absolute quantification in mass spectrometry (mass labels, isobaric labels-iTRAQ).
• 5. Determination of protein modifications
• Overview of modification types (chemical, post-translational modifications), mutations. Phosphoproteins - sample preparation and detection, localization of phosphorylations. Glycoproteins sample preparation and detection, glycan analysis.
• 6. Protein arrays (RNDr. Šárka Pospíšilová, PhD)
• Protein array types, their preparation, detection a quantification.
• 7. Proteomic applications
• Mass spectrometry and disease diagnostics (biomarker identification, protein profiling), proteomic projects in our Core lab.

Literature

• Proteome research : mass spectrometry. Edited by Peter James. Berlin: Springer-Verlag, 2001, xxi, 274 s. ISBN 3-540-67255-9-. info

Teaching methods

lecture, class discussion

Assessment methods

colloquium or oral examination

Language of instruction

Czech

Further comments (probably available only in Czech)

The course is taught annually.
The course is taught: every week.

Bi7050 Protein characterisation using mass spectrometry

Extent and Intensity

1/0/0. 1 credit(s) (plus extra credits for completion). Recommended Type of Completion: k (colloquium). Other types of completion: zk (examination).

Teacher(s)

prof. RNDr. Zbyněk Zdráhal, Dr. (lecturer)
RNDr. Hana Konečná (lecturer)
prof. RNDr. Šárka Pospíšilová, Ph.D. (lecturer)

Guaranteed by

prof. RNDr. Jiří Fajkus, CSc.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. RNDr. Zbyněk Zdráhal, Dr.

Prerequisites (in Czech)

Základní znalosti z biochemie a molekulární biologie

Course Enrolment Limitations

The course is also offered to the students of the fields other than those the course is directly associated with.

fields of study / plans the course is directly associated with

there are 26 fields of study the course is directly associated with, display

Course objectives (in Czech)

Přednáška podává studentům, především biologických oborů, stručný úvod do metod využívajících hmotnostní spektrometrii k identifikaci proteinů a jejich modifikací včetně vybraných alternativních technik a praktických příkladů.

Syllabus (in Czech)

• 1. Hmotnostní spektrometrie Princip metody, vymezení možností metody, stručný přehled instrumentace a ionizačních technik (MALDI-TOF MS, ESI-IT MS, FTMS, hybridní systémy). 2. Příprava vzorku (RNDr. Hana Konečná) Obecné zásady přípravy vzorku pro MS analýzu. Strategie zpracování proteinových vzorků (volba vhodného souboru technik vzhledem k požadovanému výsledku experimentu). 3. Základní metody identifikace proteinů Peptide mapping, MS/MS ion search, identifikace proteinů s neznámou sekvencí (de-novo sequencing), výhody a limitace jednotlivých metod, základní proteomické přístupy (bottom-up, top-down), podobnost proteinů. 4. Kvantifikace Metody relativní a absolutní kvantifikace v hmotnostní spektrometrii (hmotnostní značky, specifické značky typu iTRAQ). 5. Určování modifikací proteinů Přehled druhů modifikací (post-translační modifikace, chemické modifikace), identifikace mutací. Fosfoproteiny příprava vzorku pro analýzu fosforylovaných proteinů a jejich detekce, určení místa fosforylace. Glykoproteiny separace a detekce glykoproteinů, analýza sacharidových residuí. 6. Proteinové čipy (RNDr. Šárka Pospíšilová, PhD) Druhy proteinových čipů, jejich příprava, detekce a kvantifikace proteinů vazaných na čipech. 7. Proteomické aplikace Hmotnostní spektrometrie a diagnostika nemocí (identifikace biomarkrů, protein profiling), praktické příklady řešené na půdě PřF.

Language of instruction

Czech

Further Comments

The course is taught annually.
The course is taught: every week.

• Enrolment Statistics (recent)