The package implements a concurrent algorithm for protein grouping.

The goal of protein grouping is to find the smallest set of proteins that accurately explains the set of peptides identified from a shotgun LC-MS/MS study, following a matching of database proteins to each identified peptide.

The implemented rules for protein grouping are as follows.

• Any two proteins PT₁ and PT₂ are assigned to the same group if and only if:

  • Proteins PT₁ and PT₂ share the same set of identified peptides; OR

  • The set of identified peptides associated with PT₁ is a proper subset of the set of identified peptides associated with PT₂; such set of peptides which are associated with PT₁ are called subset peptides; proteins that are assigned to a group by virtue of subset peptides may be confidently discarded during reporting.

• If a peptide is unique to a protein PT, then protein PT is definitely identified, and it is assigned to a singleton group.

• A protein that is unassigned by any of the foregoing rules may be confidently discarded during reporting.

• A higher level grouping may be achieved by clustering any pair of groups that have a set of peptides in common.

The work of developing this package is still on-going.

The next steps will be towards a hierarchical visualisation of the formed protein groups.

Bibliography

1. A.I. Nesvizhskii and R. Aebersold, Interpretation of Shotgun Proteomic Data: The Protein Inference Problem, Mol. Cell Proteomics, 2005, 4, 1419-1440.
2. A.R. Jones, Protein Inference and Grouping, In C. Bessant (Ed.), New Developments in Mass Spectrometry, 2017, 5, 93-115.
3. V.R. Koskinen, P.A. Emery, D.M. Creasy and J.S. Cottrell, Hierarchical Clustering of Shotgun Proteomics Data, Mol. Cell Proteomics, 2011, 10.
4. A.R. Jones, M. Eisenacher, G. Mayer, O. Kohlbacher, J. Siepen, S. Hubbard, J. Selley, B. Searle, J. Shofstahl, S. Seymour, R. Julian, P.A. Binz, E.W. Deutsch, H. Hermjakob, F. Reisinger, J. Griss, J.A. Vizcaino, M. Chambers, A. Pizarro and D. Creasy, The mzIdentML Data Standard for Mass Spectrometry-based Proteomics Results, Mol. Cell Proteomics, 2012, 11, M111.014381.
5. J. Griss, A.R. Jones, T. Sachsenberg, M. Walzer, L. Gatto, J. Hartler, G.G. Thallinger, R.M. Salek, C. Steinbeck, N. Neuhauser, J. Cox, S. Neumann, J. Fan, F. Reisinger, Q.W. Xu, N. Del Toro, Y. Perez-Riverol, F. Ghali, N. Bandeira, I. Xenarios, O. Kohlbacher, J.A. Vizcaino and H. Hermjakob, The mzTab Data Exchange Format: Communicating Mass Spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience, Mol. Cell Proteomics, 2014, 13, 2765-2775.