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Cookbook:

1. Mass Spectrometry/Polymers

1.1 - Creating PeakList
1.2 - Creating PeakAnnotation
1.3 - Creating Spectrum
1.4 - Creating Protein
1.5 - Creating Peptide
1.6 - Fetching Atoms and Molecules
1.7 - Creating Modification
1.8 - Generating set of Peptides with variable modifications

2. IO

2.1 - Reading Mass Spectrometry data
2.2 - Customizing mgf reader

3. Processing

3.1 - Digesting a Protein
3.2 - Fragmenting a Peptide

4. Matching PeakLists

4.1 - Annotating a PeakList

5. Hadoop and Spark Integration

5.1 - Building a spectrum library using Hadoop
5.2 - Spark Spectrum Library Search
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