Computational methods for mass spectrometry proteomics:
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| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Chichester
Wiley
2007
|
| Subjects: | |
| Online Access: | Publisher description Table of contents only Inhaltsverzeichnis |
| Physical Description: | X, 284 S. Ill., graph. Darst. |
| ISBN: | 9780470512975 0470512970 |
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| 245 | 1 | 0 | |a Computational methods for mass spectrometry proteomics |c Ingvar Eidhammer ... |
| 264 | 1 | |a Chichester |b Wiley |c 2007 | |
| 300 | |a X, 284 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
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| 650 | 4 | |a Datenverarbeitung | |
| 650 | 4 | |a Proteomics |x Data processing | |
| 650 | 4 | |a Mass spectrometry |x Data processing | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a Proteomics |x methods | |
| 650 | 4 | |a Computational Biology |x methods | |
| 650 | 4 | |a Mass Spectrometry |x methods | |
| 700 | 1 | |a Eidhammer, Ingvar |e Sonstige |4 oth | |
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Record in the Search Index
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| adam_text | Contents
Preface ix
Acknowledgements xi
1 Protein, proteome, and proteomics 1
1.1 Primary goals for studying proteomes 1
1.2 Defining the protein 3
1.3 Protein properties - attributes and values 5
1.4 Posttranslational modifications 14
1.5 Protein sequence databases 16
1.6 Identification and characterization of proteins 18
1.7 Two approaches for bottom-up protein analysis by mass spectrometry 20
1.8 Instrument calibration and measuring errors 25
Exercises 28
Bibliographie notes 28
2 Protein Separation - 2D gel electrophoresis 31
2.1 Separation on molecular mass - SDS-PAGE 32
2.2 Separation on isoelectric point - IEF 35
2.3 Separation on mass and isoelectric point - 2D SDS-PAGE 36
2.4 2D SDS-PAGE for (complete) proteomics 37
Exercises 40
Bibliographie notes 41
3 Protein digestion 43
3.1 Experimental digestion 46
3.2 In silico digestion 50
Exercises 51
Bibliographie notes 52
4 Peptide Separation - HPLC 53
4.1 High-pressure liquid chromatography, HPLC 54
4.2 Stationary phases and Separation modes 56
4.3 Component migration and retention time 58
4.4 The shape of the peaks 59
vi CONTENTS
4.5 Chromatography used for protein Identification 60
4.6 Chromatography used for quantification 63
Exercises 63
Bibliographie notes 65
5 Fundamentals of mass spectrometry 67
5.1 The principle of mass spectrometry 67
5.2 Ionization sources 69
5.3 Mass analyzers 72
5.4 Isotopic composition of peptides 72
5.5 Fractional masses 73
5.6 The raw data 77
5.7 Mass resolution and resolving power 77
Exercises 79
Bibliographie notes 79
6 Mass spectrometry - MALDI-TOF 81
6.1 TOF analyzers and their resolution 82
6.2 Constructing the peak list 86
6.3 Peak list preprocessing 92
6.4 Peak list format 93
6.5 Automation of MALDI-TOF-MS 93
Exercises 94
Bibliographie notes 94
7 Protein Identification and characterization by MS 97
7.1 The main search procedure 98
7.2 The peptide mass comparison 102
7.3 Database search and recalibration 103
7.4 Score calculation 105
7.5 Statistical significance - the P-value 111
7.6 Characterization 115
Exercises 116
Bibliographie notes 117
8 Tandem MS or MS/MS analysis 119
8.1 Peptide fragments 120
8.2 Fragmentation techniques 123
8.3 MS/MS spectrometers 124
8.4 Different types of analyzers 125
8.5 Overview of the process for MS/MS analysis 132
8.6 Fragment ion masses and residue masses 133
8.7 Deisotoping and Charge State deconvolution 135
8.8 Precursor treatment 136
8.9 MS3 spectra 139
Exercises 139
Bibliographie notes 140
9 Fragmentation modeis 141
9.1 Chemical approach 141
9.2 Statistical approach 142
9.3 Learning (collecting statistics) 144
CONTENTS vii
9.4 The effect of amino acids on the fragmentation 149
Exercises 150
Bibliographie notes 151
10 Identification and characterization by MS/MS 153
10.1 Effect of operations (modifications, mutations) on spectra 154
10.2 Filtering and organization of the database 156
10.3 Scoring and statistical significance 157
Exercises 157
11 Spectral comparisons 159
11.1 Constructing a theoretical spectrum 159
11.2 Non-probabilistic scoring 160
11.3 Probabilistic scoring 164
11.4 Comparison with modifications 169
Exercises 176
Bibliographie notes 177
12 Sequential comparison - de novo sequenring 179
12.1 Spectrum graphs 180
12.2 Preprocessing 183
12.3 Node scores 184
12.4 Constructing the spectrum graph 185
12.5 The sequencing procedure using spectrum graphs 186
12.6 Combined spectra to improve de novo sequencing 189
Exercises 190
Bibliographie and additional notes 191
13 Database searching for de novo sequences 193
13.1 Using general sequence search programs 194
13.2 Specialized search programs 198
13.3 Peptide sequence tags 201
13.4 Comparison by threading 206
Exercises 208
Bibliographie notes 209
14 Large-scale proteomics 211
14.1 Coverage and complexity 211
14.2 Selecting a representative peptide sample - COFRADIC 212
14.3 Separating peptides into fractions 215
14.4 Producing MS/MS spectra 216
14.5 Spectrum filtering 217
14.6 Spectrum clustering 220
14.7 Searching the database 227
14.8 UMS 227
Exercises 228
Bibliographie notes 228
15 Quantitative MS-based proteomics 229
15.1 Defining the quantification task 229
15.2 mRNA and protein quantification 23°
15.3 Quantification of peaks 230
viii CONTENTS
15.4 Normalization 231
15.5 Different methods for quantification 232
15.6 Label-free quantification 232
15.7 Label-based quantification 236
15.8 Variance-stabilizing transformations 2^0
15.9 Dynamic ränge 2^0
15.10 Inferring relative quantity from peptide Identification scores 2*0
15.11 Absolute quantification methods 2^1
Bibliographie notes 2^2
16 Peptides to proteins 2*3
16.1 Peptides and proteins 2^3
16.2 Protein identification using peptide masses: an example revisited 2*3
16.3 Minimal and maximal explanatory sets 2^6
Bibliographie notes 2^7
17 Top-down proteomics 2*
17.1 Separation of intact proteins 2*9
17.2 Ionization of intact proteins 2^-9
17.3 Resolution and aecuraey requirements for Charge State determination
and mass calculation 250
17.4 Fragmentation of intact proteins 251
17.5 Charges of the fragments 252
17.6 Protein identification 252
17.7 Protein characterization - detecting modifications 252
17.8 Problems with top-down approach 253
Exercises 253
Bibliographie notes 254
18 Standards 255
18.1 Standard creation 255
18.2 Standards from a proteomics perspective 256
18.3 The Proteomics Standards Initiative 260
18.4 Mass spectrometry Standards 260
18.5 Modification Standards 262
18.6 Identification Standards 262
Bibliographie notes 263
Bibliography 265
Index 277
|
| adam_txt |
Contents
Preface ix
Acknowledgements xi
1 Protein, proteome, and proteomics 1
1.1 Primary goals for studying proteomes 1
1.2 Defining the protein 3
1.3 Protein properties - attributes and values 5
1.4 Posttranslational modifications 14
1.5 Protein sequence databases 16
1.6 Identification and characterization of proteins 18
1.7 Two approaches for bottom-up protein analysis by mass spectrometry 20
1.8 Instrument calibration and measuring errors 25
Exercises 28
Bibliographie notes 28
2 Protein Separation - 2D gel electrophoresis 31
2.1 Separation on molecular mass - SDS-PAGE 32
2.2 Separation on isoelectric point - IEF 35
2.3 Separation on mass and isoelectric point - 2D SDS-PAGE 36
2.4 2D SDS-PAGE for (complete) proteomics 37
Exercises 40
Bibliographie notes 41
3 Protein digestion 43
3.1 Experimental digestion 46
3.2 In silico digestion 50
Exercises 51
Bibliographie notes 52
4 Peptide Separation - HPLC 53
4.1 High-pressure liquid chromatography, HPLC 54
4.2 Stationary phases and Separation modes 56
4.3 Component migration and retention time 58
4.4 The shape of the peaks 59
vi CONTENTS
4.5 Chromatography used for protein Identification 60
4.6 Chromatography used for quantification 63
Exercises 63
Bibliographie notes 65
5 Fundamentals of mass spectrometry 67
5.1 The principle of mass spectrometry 67
5.2 Ionization sources 69
5.3 Mass analyzers 72
5.4 Isotopic composition of peptides 72
5.5 Fractional masses 73
5.6 The raw data 77
5.7 Mass resolution and resolving power 77
Exercises 79
Bibliographie notes 79
6 Mass spectrometry - MALDI-TOF 81
6.1 TOF analyzers and their resolution 82
6.2 Constructing the peak list 86
6.3 Peak list preprocessing 92
6.4 Peak list format 93
6.5 Automation of MALDI-TOF-MS 93
Exercises 94
Bibliographie notes 94
7 Protein Identification and characterization by MS 97
7.1 The main search procedure 98
7.2 The peptide mass comparison 102
7.3 Database search and recalibration 103
7.4 Score calculation 105
7.5 Statistical significance - the P-value 111
7.6 Characterization 115
Exercises 116
Bibliographie notes 117
8 Tandem MS or MS/MS analysis 119
8.1 Peptide fragments 120
8.2 Fragmentation techniques 123
8.3 MS/MS spectrometers 124
8.4 Different types of analyzers 125
8.5 Overview of the process for MS/MS analysis 132
8.6 Fragment ion masses and residue masses 133
8.7 Deisotoping and Charge State deconvolution 135
8.8 Precursor treatment 136
8.9 MS3 spectra 139
Exercises 139
Bibliographie notes 140
9 Fragmentation modeis 141
9.1 Chemical approach 141
9.2 Statistical approach 142
9.3 Learning (collecting statistics) 144
CONTENTS vii
9.4 The effect of amino acids on the fragmentation 149
Exercises 150
Bibliographie notes 151
10 Identification and characterization by MS/MS 153
10.1 Effect of operations (modifications, mutations) on spectra 154
10.2 Filtering and organization of the database 156
10.3 Scoring and statistical significance 157
Exercises 157
11 Spectral comparisons 159
11.1 Constructing a theoretical spectrum 159
11.2 Non-probabilistic scoring 160
11.3 Probabilistic scoring 164
11.4 Comparison with modifications 169
Exercises 176
Bibliographie notes 177
12 Sequential comparison - de novo sequenring 179
12.1 Spectrum graphs 180
12.2 Preprocessing 183
12.3 Node scores 184
12.4 Constructing the spectrum graph 185
12.5 The sequencing procedure using spectrum graphs 186
12.6 Combined spectra to improve de novo sequencing 189
Exercises 190
Bibliographie and additional notes 191
13 Database searching for de novo sequences 193
13.1 Using general sequence search programs 194
13.2 Specialized search programs 198
13.3 Peptide sequence tags 201
13.4 Comparison by threading 206
Exercises 208
Bibliographie notes 209
14 Large-scale proteomics 211
14.1 Coverage and complexity 211
14.2 Selecting a representative peptide sample - COFRADIC 212
14.3 Separating peptides into fractions 215
14.4 Producing MS/MS spectra 216
14.5 Spectrum filtering 217
14.6 Spectrum clustering 220
14.7 Searching the database 227
14.8 UMS 227
Exercises 228
Bibliographie notes 228
15 Quantitative MS-based proteomics 229
15.1 Defining the quantification task 229
15.2 mRNA and protein quantification 23°
15.3 Quantification of peaks 230
viii CONTENTS
15.4 Normalization 231
15.5 Different methods for quantification 232
15.6 Label-free quantification 232
15.7 Label-based quantification 236
15.8 Variance-stabilizing transformations 2^0
15.9 Dynamic ränge 2^0
15.10 Inferring relative quantity from peptide Identification scores 2*0
15.11 Absolute quantification methods 2^1
Bibliographie notes 2^2
16 Peptides to proteins 2*3
16.1 Peptides and proteins 2^3
16.2 Protein identification using peptide masses: an example revisited 2*3
16.3 Minimal and maximal explanatory sets 2^6
Bibliographie notes 2^7
17 Top-down proteomics 2*'
17.1 Separation of intact proteins 2*9
17.2 Ionization of intact proteins 2^-9
17.3 Resolution and aecuraey requirements for Charge State determination
and mass calculation 250
17.4 Fragmentation of intact proteins 251
17.5 Charges of the fragments 252
17.6 Protein identification 252
17.7 Protein characterization - detecting modifications 252
17.8 Problems with top-down approach 253
Exercises 253
Bibliographie notes 254
18 Standards 255
18.1 Standard creation 255
18.2 Standards from a proteomics perspective 256
18.3 The Proteomics Standards Initiative 260
18.4 Mass spectrometry Standards 260
18.5 Modification Standards 262
18.6 Identification Standards 262
Bibliographie notes 263
Bibliography 265
Index 277 |
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| spelling | Computational methods for mass spectrometry proteomics Ingvar Eidhammer ... Chichester Wiley 2007 X, 284 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Datenverarbeitung Proteomics Data processing Mass spectrometry Data processing Bioinformatics Proteomics methods Computational Biology methods Mass Spectrometry methods Eidhammer, Ingvar Sonstige oth http://www.loc.gov/catdir/enhancements/fy0745/2007040536-d.html Publisher description http://www.loc.gov/catdir/enhancements/fy0745/2007040536-t.html Table of contents only HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016476864&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computational methods for mass spectrometry proteomics Datenverarbeitung Proteomics Data processing Mass spectrometry Data processing Bioinformatics Proteomics methods Computational Biology methods Mass Spectrometry methods |
| title | Computational methods for mass spectrometry proteomics |
| title_auth | Computational methods for mass spectrometry proteomics |
| title_exact_search | Computational methods for mass spectrometry proteomics |
| title_exact_search_txtP | Computational methods for mass spectrometry proteomics |
| title_full | Computational methods for mass spectrometry proteomics Ingvar Eidhammer ... |
| title_fullStr | Computational methods for mass spectrometry proteomics Ingvar Eidhammer ... |
| title_full_unstemmed | Computational methods for mass spectrometry proteomics Ingvar Eidhammer ... |
| title_short | Computational methods for mass spectrometry proteomics |
| title_sort | computational methods for mass spectrometry proteomics |
| topic | Datenverarbeitung Proteomics Data processing Mass spectrometry Data processing Bioinformatics Proteomics methods Computational Biology methods Mass Spectrometry methods |
| topic_facet | Datenverarbeitung Proteomics Data processing Mass spectrometry Data processing Bioinformatics Proteomics methods Computational Biology methods Mass Spectrometry methods |
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