A5035084784- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Web Data Mining and Analysis
- Microbial Metabolism and Applications
- Protein Hydrolysis and Bioactive Peptides
- Peanut Plant Research Studies
- Recommender Systems and Techniques
- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- 14-3-3 protein interactions
- Ubiquitin and proteasome pathways
- Pharmacological Effects of Natural Compounds
- Data Management and Algorithms
- Bee Products Chemical Analysis
- Natural product bioactivities and synthesis
- Computational Drug Discovery Methods
Institute of Computing Technology
2018-2025
University of Chinese Academy of Sciences
2021-2025
Jingdong (China)
2025
Chinese Academy of Sciences
2018-2024
Abstract We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With two-stage open strategy facilitated by fragment indexing, 2 is ~40 times faster than 1 3~10 Kojak. Furthermore, using simulated datasets, synthetic 15 N metabolically labeled entrapment databases, four analysis methods were designed to evaluate the credibility ten state-of-the-art engines. This systematic evaluation shows that outperforms these in...
A key challenge in personalized product search is to capture user’s preferences. Recent work attempted model sequences of user historical behaviors, i.e., purchase histories, build profiles and personalize results accordingly. Although these approaches have demonstrated promising retrieval performances, we notice that most them focus solely on the intra-sequence interactions between items. However, as there usually a small amount behavior data, learned by could be very sensitive noise...
Ubiquitin-like proteins (UBLs) constitute a family of evolutionarily conserved that share similarities with ubiquitin in 3D structures and modification mechanisms. For most UBLs including Small-Ubiquitin-like Modifiers (SUMO), their sites on substrate cannot be identified using the mass spectrometry-based method has been successful for identifying ubiquitination sites, unless UBL protein is mutated accordingly. To identify without having to mutate UBL, we have developed dedicated search...
Disulfide bonds are vital for protein functions, but locating the linkage sites has been a challenge in chemistry, especially when quantity of sample is small or complexity high. In 2015, our laboratory developed sensitive and efficient method mapping disulfide from simple complex samples (Lu et al. Nat Methods 12:329, 2015). This based on liquid chromatography-mass spectrometry (LC-MS) powerful data analysis software tool named pLink. To facilitate application this method, we present...
In cross-linking mass spectrometry, the identification of cross-linked peptide pairs heavily relies on ability a database search engine to measure similarities between experimental and theoretical MS/MS spectra. However, lack accurate ion intensities in spectra impairs performance engines, particular, proteome scales. Here we introduce pDeepXL, deep neural network predict pairs. To train used transfer-learning technique because it facilitated training with limited benchmark data Test results...
When it comes to mass spectrometry data analysis for identification of peptide pairs linked by N-hydroxysuccinimide (NHS) ester cross-linkers, search engines bifurcate in their setting cross-linkable sites. Some restrict NHS sites lysine (K) and protein N-terminus, referred as K only short, whereas others additionally include serine (S), threonine (T), tyrosine (Y) default. Here, amino acids with chemically inert side chains such glycine (G), valine (V), leucine (L) sites, which serves a...
Ubiquitin-like proteins (UBLs) constitute a family of evolutionarily conserved that share similarities with ubiquitin in 3D structures and modification mechanisms. For most UBLs including Small-Ubiquitin-like Modifiers (SUMO), their sites on substrate cannot be identified using the mass spectrometry-based method has been successful for identifying ubiquitination sites, unless UBL protein is mutated accordingly. To identify without having to mutate UBL, we have developed dedicated search...