We developed the tool, GenoMS, for sequencing small samples of proteins. Protein sequence templates (i.e. proteins or genomic sequences that are similar to the target protein) are identified using the database search tool InsPecT. The templates are then used to recruit, align, and de novo sequence regions of the target protein that have diverged from the database or are missing. We used GenoMS to reconstruct the full sequence of an antibody by using spectra acquired from multiple digests using different proteases. Antibodies are a prime example of proteins that confound standard database identification techniques. The mature antibody genes result from… Read more »

Nonribosomal peptides (NRPs) are of great pharmacological importance, but there is currently no technology for high-throughput NRP ‘dereplication’ and sequencing. We used multistage mass spectrometry followed by spectral alignment algorithms for sequencing of cyclic NRPs. We also developed an algorithm for comparative NRP dereplication that establishes similarities between newly isolated and previously identified similar but nonidentical NRPs, substantially reducing dereplication efforts. The homepage for this project can be found here.

Our study of the Arabidopsis proteome through tandem mass spectrometry revealed over 18,000 novel peptides not in the TAIR7 genome annotation release. Using Inspect, we identified over 144,000 peptides from 3 sequence databases; the six-frame translation of the Arabidopsis genome, an exon-graph based on ab initio gene predictions, and the TAIR7 proteome. From the novel peptides we predicted over 700 new gene models and over 600 corrections to current gene models. The peptides and predicted models can be accessed here.

Multistage mass spectrometry (collecting multiple MS^3 spectra from each MS^2 spectrum) and accurate precursor masses (but inaccurate fragment masses) have been demonstrated to lead to significant gains in peptide identification via database search but have had a limited impact in de novo peptide sequencing. Our Multi-stage Spectral Networks package addresses both of these in a rigorous probabilistic framework for analyzing spectra of overlapping peptides, resulting in both accurate de novo peptide sequencing from multistage mass spectra (despite the inferior quality of MS^3 spectra) and improved interpretation of spectral networks. Additional details and the open-source package are available here.

Phosphate Localization Score is an algorithm which determines the confidence of the placement of a phosphate on a given residue. This method is similar to the AScore, and is described in Albuquerque et al., Mol Cell Proteomics 2008. The program is integrated with the Inspect package, download available here. A tutorial for using the program is in the Inspect documentation, here.

MS-Dictionary is a software to generate all plausible de novo interpretations of a tandem mass spectrum(spectral dictionary) and matches them against a protein database quickly. It enables proteogenomic searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches.

MS-GF is a software for computing the generating function of a tandem mass spectrum.The generating functions and their derivatives represent new features of tandem mass spectra that improve peptide identifications. Further, they enable one to rigorously compute error rates of peptide identifications and get better sensitivity-specificity trade-off of existing MS/MS search tools.

MS-Clustering is a new program aimed at improving the analysis large MS/MS datasets by removing many of their redundant or low quality spectra. MS-Clustering is capable of reducing the number of spectra submitted for analysis from a large 10+ million dataset by 90% while increasing the number peptide/protein identifications by up to 10%.

Spectral networks are a novel approach to the identification of MS/MS spectra that detects and combines spectra from overlapping peptides or modified variants of the same peptide. This approach allows for the blind indentification of unexpected post-translational modifications and highly modified peptides. The spectral networks software package is now available in open-source and Windows-binary versions.