Learn More
SUMMARY Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported(More)
O-glycosylation is one of the most important, frequent and complex post-translational modifications. This modification can activate and affect protein functions. Here, we present three support vector machines models based on physical properties, 0/1 system, and the system combining the above two features. The prediction accuracies of the three models have(More)
MOTIVATION The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS This paper provides a promising approach(More)
a r t i c l e i n f o a b s t r a c t Keywords: Rotating Bose–Einstein condensate Gross–Pitaevskii equation Vortex lattices Strong repulsive interaction regime Angular momentum rotation We propose an efficient and spectrally accurate numerical method for computing vortex lattices in rapid rotating Bose–Einstein condensates (BECs), especially with strong(More)
A number of different approaches have been proposed to predict elemental component formulas (or molecular formulas) of molecular ions in low and medium resolution mass spectra. Most of them rely on isotope patterns, enumerate all possible formulas for an ion, and exclude certain formulas violating chemical constraints. However, these methods cannot be well(More)
MOTIVATION One of the major problems in shotgun proteomics is the low peptide coverage when analyzing complex protein samples. Identifying more peptides, e.g. non-tryptic peptides, may increase the peptide coverage and improve protein identification and/or quantification that are based on the peptide identification results. Searching for all potential(More)
Due to the compartmentalization within scientific disciplines and the fact that modern scientific methods are extensively used in CAM research, it appears that there has been a huge disconnect between clinical studies and preclinical studies including authentication, quality control, pharmacology, and toxicology of CAM agents. In this special issue, we(More)
Tandem mass spectrometry (MS/MS) has become increasingly important and indispensable in high-throughput proteomics for identifying complex protein mixtures. Database searching is the standard method to accomplish this purpose. A key sub-routine, peptide identification, is used to generate a list of candidate peptides from a protein database according to an(More)