Hierarchical Clustering of Shotgun Proteomics Data

A new result report for Mascot search results is described. A greedy set cover algorithm is used to create a minimal set of proteins, which is then grouped into families on the basis of shared peptide matches. Protein families with multiple members are represented by dendrograms, generated by hierar...

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Bibliographic Details
Published in:Molecular & cellular proteomics 2011-06, Vol.10 (6), p.M110.003822-M110.003822, Article M110.003822
Main Authors: Koskinen, Ville R., Emery, Patrick A., Creasy, David M., Cottrell, John S.
Format: Article
Language:English
Subjects:
Algorithms
Amino Acid Sequence
Cluster Analysis
Computer Simulation
Databases, Protein
Models, Molecular
Molecular Sequence Data
Molecular Weight
Peptide Fragments - chemistry
Proteomics - methods
Sequence Analysis, Protein - methods
Tandem Mass Spectrometry - methods
Technological Innovation and Resources
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Summary:A new result report for Mascot search results is described. A greedy set cover algorithm is used to create a minimal set of proteins, which is then grouped into families on the basis of shared peptide matches. Protein families with multiple members are represented by dendrograms, generated by hierarchical clustering using the score of the nonshared peptide matches as a distance metric. The peptide matches to the proteins in a family can be compared side by side to assess the experimental evidence for each protein. If the evidence for a particular family member is considered inadequate, the dendrogram can be cut to reduce the number of distinct family members.
ISSN:1535-9476
1535-9484
DOI:10.1074/mcp.M110.003822