Spectral Networks

The spectral networks paradigm pioneered at CCMS differs from the mainstream paradigm for interpretation of tandem mass spectra in three fundamental ways. First, spectral networks are based on matching spectra against other spectra instead of against protein sequences. Second, spectral networks find spectra from related peptides (e.g., modified/unmodified or overlapping-sequence variants) even before considering their possible identifications. Third, spectral networks determine consensus identifications for sets of spectra from related peptides instead of separately attempting to identify each spectrum at a time.

This paradigm has now been extended from peptides to Molecular Networks of any class of molecules.

Spectral Networks

Software Tools & Datasets

MetaSPS: Tool home page
Molecular Networks: Tool home page ProteoSAFe workflow
Tremolo: Tool home page ProteoSAFe workflow

Key Publications

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Moree WJ, Phelan VV, Wu CH, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13811-6. doi: 10.1073/pnas.1206855109.
The generating function approach for peptide identification in spectral networks Guthals A., Christina B. Bandeira N. Research in Computational Molecular Biology, Lecture Notes in Computer Science; (8394) 85-99
Protein identification by spectral networks analysis. Bandeira N. Methods Mol Biol. 2011;694:151-68. doi: 10.1007/978-1-60761-977-2_11.
Mass spectral molecular networking of living microbial colonies. Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):E1743-52. doi: 10.1073/pnas.1203689109. Epub 2012 May 14.
Shotgun protein sequencing with meta-contig assembly. Guthals A, Clauser KR, Bandeira N. Mol Cell Proteomics. 2012 Oct;11(10):1084-96.
Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. Guthals A, Clauser KR, Frank AM, Bandeira N. J Proteome Res. 2013 Jun 7;12(6):2846-57.
View All CCMS Publictions

After substantial algorithmic developments, spectral networks have now delivered the longest (10× longer than single-spectrum sequencing) and most accurate (98% sequencing accuracy) de novo sequences to date (see MetaSPS), confirmed the new route for discovery of unexpected post-translational modifications and highly-modified peptides, enabled the automated sequencing of non-linear (e.g., cyclic) non-ribosomal peptides (see Antibiotics Sequencing) and are now defining a novel molecular spectral networks approach for mapping the entire molecular output of any biological system suitable for analysis with tandem mass spectrometry (see Molecular Networks).