Generating and analyzing overlapping peptides through multienzymatic digestion is an efficient procedure for de novo protein using from bottom-up mass spectrometry (MS). Despite improved instrumentation and software, de novo MS data analysis remains ...
Region of interest (ROI) extraction is a fundamental step in analyzing metabolomic datasets acquired by liquid chromatography-mass spectrometry (LC-MS). However, noises and backgrounds in LC-MS data often affect the quality of extracted ROIs. Therefo...
Data-independent acquisition (DIA) of tandem mass spectrometry spectra has emerged as a promising technology to improve coverage and quantification of proteins in complex mixtures. The success of DIA experiments is dependent on the quality of spectra...
In tandem mass spectrometry-based proteomics, proteins are digested into peptides by specific protease(s), but generally only a fraction of peptides can be detected. To characterize detectable proteotypic peptides, we have developed a series of metho...
Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is a powerful analytical tool used for adulteration inspection. Nevertheless, it is a challenging task to identify illegal adulterants that are not included in the library or are unexp...
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFrag...
Predicting peptide detectability is useful in a variety of mass spectrometry (MS)-based proteomics applications, particularly targeted proteomics. However, most machine learning-based computational methods have relied solely on information from the p...
The development of a fast, cost-effective, and efficient microextraction by packed sorbent setup was achieved by combining affordable laboratory-repackable devices of microextraction with a high-throughput cartesian robot. This setup was evaluated fo...
Journal of chemical information and modeling
37725368
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method depends o...
First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the 'gold standard' knowledge resource for drug, drug-target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and cl...