Proteomics Data Analysis
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Part I: Data Analysis for Gel-Based Proteomics
1. Two-Dimensional Gel Electrophoresis Image Analysis
Elisa Robotti, Elisa Cal? and Emilio Marengo
2. Chemometric Tools for 2D-PAGE Data Analysis
Elisa Robotti, Elisa Cal? and Emilio Marengo
Part II: Data Analysis for Gel-Free Proteomics
3. Software Options for the Analysis of MS Proteomic Data
Avinash Yadav, Federica Marini, Alessandro Cuomo, and Tiziana Bonaldi
4. Analysis of Label-Based Quantitative Proteomics Data Using IsoProt
Johannes Griss and Veit Schw鄝mle
5. Quantification of Changes in Protein Expression Using SWATH Proteomics
Clarissa Braccia, Nara Liessi, and Andrea Armirotti
6. Data Processing and Analysis for DIA-Based Phosphoproteomics Using Spectronaut
Ana Martinez-Val, Dorte Breinholdt Bekker-Jensen, Alexander Hogrebe, and Jesper Velgaard Olsen
7. Enhanced Glycopeptide Identification Using a GlyConnect Compozitor-Derived Glycan Composition File
Julien Mariethoz, Catherine Hayes, and Fr嶮廨ique Lisacek
8. Elaboration Pipeline for the Management of MALDI-MS Imaging Datasets
Andrew Smith, Isabella Piga, Vanna Denti, Clizia Chinello, and Fulvio Magni
9. Features Selection and Extraction in Statistical Analysis of Proteomics Datasets
Marta Lualdi and Mauro Fasano
Part III: Proteomics Data Interpretation
10. ORA, FCS, and PT Strategies in Functional Enrichment Analysis
Marco Fernandes and Holger Husi
11. A Strategy for the Annotation and GO Enrichment Analysis of a List of Differentially Expressed Proteins Using ProteoRE
Florence Combes, Valentin Loux, and Yves Vandenbrouck
12. Protein Subcellular Localization Prediction
Elettra Barberis, Emilio Marengo, and Marcello Manfredi
13. Protein Secretion Prediction Tools and Extracellular Vesicles Databases
Daniela Cecconi, Claudia Di Carlo, and Jessica Brandi
14. Databases for Protein-Protein Interactions
Natsu Nakajima, Tatsuya Akutsu, and Ryuichiro Nakato
15. Machine and Deep Learning for Prediction of Subcellular Localization
Gaofeng Pan, Chao Sun, Zijun Liao, and Jijun Tang
16. Deep Learning for Protein-Protein Interaction Site Prediction
Arian R. Jamasb, Ben Day, Cătălina Cangea, Pietro Li? and Tom L. Blundell
Part IV:
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