http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
Bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, Proteome Informatics will provide a detailed introduction to the main informatics topics that underpin the various LC-MS/MS protocols used for protein identification and quantitation.
Cover; Proteome Informatics; Acknowledgements; Contents; Chapter 1 -- Introduction to Proteome Informatics; 1.1 Introduction; 1.2 Principles of LC-MS/MS Proteomics; 1.2.1 Protein Fundamentals; 1.2.2 Shotgun Proteomics; 1.2.3 Separation of Peptides by Chromatography; 1.2.4 Mass Spectrometry; 1.3 Identification of Peptides and Proteins; 1.4 Protein Quantitation; 1.5 Applications and Downstream Analysis; 1.6 Proteomics Software; 1.6.1 Proteomics Data Standards and Databases; 1.7 Conclusions; Acknowledgements; References; Section I -- Protein Identification; Chapter 2 -- De novo Peptide Sequencing
2.1 Introduction2.2 Manual De novo Sequencing; 2.3 Computer Algorithms; 2.3.1 Search Tree Pruning; 2.3.2 Spectrum Graph; 2.3.3 PEAKS Algorithm; 2.4 Scoring Function; 2.4.1 Likelihood Ratio; 2.4.2 Utilization of Many Ion Types; 2.4.3 Combined Use of Different Fragmentations; 2.4.4 Machine Learning; 2.4.5 Amino Acid Score; 2.5 Computer Software; 2.5.1 Lutefisk; 2.5.2 Sherenga; 2.5.3 PEAKS; 2.5.4 PepNovo; 2.5.5 DACSIM; 2.5.6 NovoHMM; 2.5.7 MSNovo; 2.5.8 PILOT; 2.5.9 pNovo; 2.5.10 Novor; 2.6 Conclusion: Applications and Limitations of De novo Sequencing
2.6.1 Sequencing Novel Peptides and Detecting Mutated Peptides2.6.2 Assisting Database Search; 2.6.3 De novo Protein Sequencing; 2.6.4 Unspecified PTM Characterization; 2.6.5 Limitations; Acknowledgements; References; Chapter 3 -- Peptide Spectrum Matching via Database Search and Spectral Library Search; 3.1 Introduction; 3.2 Protein Sequence Databases; 3.3 Overview of Shotgun Proteomics Method; 3.4 Collision Induced Dissociation Fragments Peptides in Predictable Ways; 3.5 Overview of Database Searching; 3.6 MyriMatch Database Search Engine; 3.6.1 Spectrum Preparation
3.13 Search Results Vary Between Various Database Search Engines and Different Peptide Identification Search Strategies3.14 Conclusion; References; Chapter 4 -- PSM Scoring and Validation; 4.1 Introduction; 4.2 Statistical Scores and What They Mean; 4.2.1 Statistical Probability p-Values and Multiple Testing; 4.2.2 Expectation Scores; 4.2.3 False Discovery Rates; 4.2.4 q-Values; 4.2.5 Posterior Error Probability; 4.2.6 Which Statistical Measure to Use and When; 4.2.7 Target Decoy Approaches for FDR Assessment; 4.3 Post-Search Validation Tools and Methods; 4.3.1 Qvality; 4.3.2 PeptideProphet
3.6.2 Peptide Harvesting from Database3.6.3 Comparing Experimental MS/MS with Candidate Peptide Sequences; 3.7 Accounting for Post-Translational Modifications During Database Search; 3.8 Reporting of Database Search Peptide Identifications; 3.9 Spectral Library Search Concept; 3.10 Peptide Spectral Libraries; 3.11 Overview of Spectral Library Searching; 3.12 Pepitome Spectral Library Search Engine; 3.12.1 Experimental MS2 Spectrum Preparation; 3.12.2 Library Spectrum Harvesting and Spectrum-Spectrum Matching; 3.12.3 Results Reporting
[England] : Royal Society of Chemistry, [2017]
New developments in mass spectrometry ; 5