Shotgun Protein Sequencing

from Tandem Mass Spectra (MS/MS) data

The analysis of mass spectrometry data is still largely based on identification of single MS/MS spectra and does not attempt to make use of the extra information available in multiple MS/MS spectra from partially or completely overlapping peptides. Analysis of MS/MS spectra from multiple overlapping peptides opens up the possibility of assembling MS/MS spectra into entire proteins, similarly to the assembly of overlapping DNA reads into entire genomes. Our open-source software tool recovers all or parts of the protein sequence through clustering, pairwise alignment, assembly and de-novo interpretation of the input MS/MS spectra.

Now available as an open source Matlab package

Please contact bandeira at for any comments/questions.

UCSD Computational MS/MS Research Group