Index
1 Introduction... 1
2 Proteomics and bioinformatics ... 4
2.1 Proteomics... 5
2.2 Genome and proteome ... 9
2.2.1 DNA... 10
2.2.2 From DNA to mRNA: Transcription... 11
2.2.3 From mRNA to proteins: Translation ... 13
2.2.4 Protein modification... 14
2.3 Proteomics data analysis ... 14
2.3.1 Separation technique: 2D gel electrophoresis... 15
2.3.2 Separation technique: MudPIT ... 17
2.3.3 Protein detection by Mass Spectrometry ... 19
2.3.4 Mass analyser technologies... 22
2.3.5 Ion fragmentation... 26
2.4 Algorithms for protein identification ... 28
2.4.1 Peptide mass fingerprinting ... 29
2.4.2 Tandem MS... 30
2.4.3 De novo sequencing... 30
2.5 Scoring methods... 31
2.6 Bioinformatics in proteomics... 34
2.7 Summary ... 36
3 Pipelines and GAPP... 37
3.1 Repositories ... 38
3.1.1 Search engine pipelines... 39
3.1.2 Data formats... 42
3.1.3 Data submission ... 44
3.1.4 Data-mining and visualisation ... 45
3.2 GAPP ... 48
3.3 GAPP Overview... 49
3.3.1 GAPP Search engine pipeline... 52
3.3.2 GAPP data formats and data submission ... 55
3.3.3 GAPP data mining and visualisation ... 56
3.4 Comparison of GAPP against the main repositories... 57
3.5 GAPP weaknesses... 59
3.6 Summary ... 61
4 GAPP Novel Data Views... 63
4.1 GAPP database... 65
4.2 GAPP Data Views... 68
4.3 Experiment View ... 69
4.3.1 Metadata ... 71
4.3.2 Search parameters ... 73
4.3.3 Proteins identified ... 75
4.3.4 Further information... 76
4.4 Protein View ... 77
4.4.1 Sequence ... 81
4.4.2 Description... 82
4.4.3 Gene Ontology description ... 83
4.4.4 Statistics ... 84
4.4.5 Modifications ... 88
4.4.6 Peptide coverage ... 90
4.4.7 Other information... 93
4.5 Differential View ... 94
4.5.1 Selection of proteins ... 95
4.5.2 Table creation... 100
4.5.3 Gene Ontology ... 102
4.5.4 GO vocabularies: Biological process, cellular component and molecular function ... 103
4.5.5 Gene Ontology database ... 111
4.5.6 Algorithm for the filling of the Gene Ontology database in GAPP. 113 4.5.7 Filtering of the proteins... 118
4.6 Summary ... 120
5 Conclusions... 121
6.References... 124
Acknowledgments... 126
