A5100728204- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Metabolomics and Mass Spectrometry Studies
- Glycosylation and Glycoproteins Research
- Machine Learning in Bioinformatics
- Security and Verification in Computing
- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Protein Hydrolysis and Bioactive Peptides
- Biotin and Related Studies
- RNA and protein synthesis mechanisms
- Cloud Computing and Resource Management
- Biopolymer Synthesis and Applications
- Advanced Malware Detection Techniques
- Animal Nutrition and Physiology
- Wastewater Treatment and Nitrogen Removal
- Bacillus and Francisella bacterial research
- Anaerobic Digestion and Biogas Production
- Evolution and Genetic Dynamics
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Steroid Chemistry and Biochemistry
- Plant nutrient uptake and metabolism
- Physical Unclonable Functions (PUFs) and Hardware Security
- Network Security and Intrusion Detection
Beihang University
2020-2025
Chinese Academy of Sciences
2010-2024
Institute of Computing Technology
2010-2024
BGI Group (China)
2021-2024
BGI Research
2024
Jiangnan University
2020-2021
Hebei Academy of Sciences
2021
University of Science and Technology Beijing
2021
Tianjin Economic-Technological Development Area
2021
Institute of Information Engineering
2016-2020
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...
The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity glycosylation, current overall throughput, data quality accessibility glycopeptide lack behind those routine proteomic analyses. Here, we propose workflow for high-throughput N-glycopeptides at proteome scale using stepped-energy fragmentation dedicated search engine. pGlyco 2.0 conducts comprehensive control including false discovery rate evaluation all three...
De novo peptide sequencing has improved remarkably in the past decade as a result of better instruments and computational algorithms. However, de can correctly interpret only approximately 30% high- medium-quality spectra generated by collision-induced dissociation (CID), which is much less than database search. This mainly due to incomplete fragmentation overlap different ion series CID spectra. In this study, we show that higher-energy collisional (HCD) great help because it produces high...
To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing biotin tag for affinity purification, cleavage site to separate cross-linked peptides away from after enrichment, and spacer arm that can be labeled stable isotopes quantitation. By locating the flexible on surface 70S ribosome, show this trifunctional is effective at attaining structural information not easily attainable by crystallography...
Confident characterization of the microheterogeneity protein glycosylation through identification intact glycopeptides remains one toughest analytical challenges for glycoproteomics. Recently proposed mass spectrometry (MS)-based methods still have some defects such as lack false discovery rate (FDR) analysis glycan and sufficient fragmentation information peptide identification. Here we pGlyco, a novel pipeline by using complementary MS techniques: 1) HCD-MS/MS followed product-dependent...
Quantification of proteomes by mass spectrometry has proven to be useful study human pathology recapitulated in cellular or animal models disease. Enriching and quantifying newly synthesized proteins (NSPs) at set time points the potential identify important early regulatory expression changes associated with disease states perturbations. NSP can enriched from employing pulsed introduction noncanonical amino acid, azidohomoalanine (AHA). We demonstrate that AHA feed mice label multiple...
There has been tremendous progress in top-down proteomics (TDP) the past 5 years, particularly intact protein separation and high-resolution mass spectrometry. However, bioinformatics to deal with large-scale spectra lagged behind, both algorithmic research software development. In this study, we developed pTop 1.0, a novel tool significantly improve accuracy efficiency of spectral data analysis TDP. The precursor offers crucial clues infer potential post-translational modifications...
Large-scale intact glycopeptide identification has been advanced by software tools. However, tools for quantitative analysis remain lagging behind, which hinders exploring the differential site-specific glycosylation. Here, we report pGlycoQuant, a generic tool both primary and tandem mass spectrometry-based quantitation. pGlycoQuant advances in matching through applying deep learning model that reduces missing values 19-89% compared with Byologic, MSFragger-Glyco, Skyline, Proteome...
Abstract Determining the monoisotopic peak of a precursor is first step in interpreting mass spectra, which basic but non‐trivial. The reason that isolation window precursor, other peaks interfere with determination peak, leading to wrong mass‐to‐charge ratio or charge state. Here we propose method, named pParse, export most probable for precursors, including co‐eluted precursors. We use relationship between position highest and detect candidate clusters. Then, extract three features sort...
Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly modeling protein structures. However, experimentally identified cross-links are sometimes incompatible known structure of a protein, as distance calculated between far exceeds maximum length cross-linker. The discrepancies may persist even after eliminating potentially false excluding intermolecular ones. Thus "over-length" arise from alternative...
Abstract Urinary proteomics is emerging as a potent tool for detecting sensitive and non-invasive biomarkers. At present, the comparability of urinary data across diverse liquid chromatography−mass spectrometry (LC-MS) platforms remains an area that requires investigation. In this study, we conduct comprehensive evaluation proteome multiple LC-MS platforms. To systematically analyze assess quality large-scale data, develop control (QC) system named MSCohort, which extracted 81 metrics...
Cholangiocarcinoma (CCA) is the second most common primary liver cancer and characterized by huge heterogeneity, difficult diagnosis, poor prognosis. Fibrosis-associated heterogeneity in CCA serves as an indicator of malignant progression cancer; however, a precise approach to deciphering fibrosis still lacking. Typically, tissue proteome profiled analyzing bulk tissues, which gives average results different cell types, especially for tissues cells occupy very small proportion. Laser...
In recent years, electron transfer dissociation (ETD) has enjoyed widespread applications from sequencing of peptides with or without post-translational modifications to top-down analysis intact proteins. However, peptide identification rates ETD spectra compare poorly those collision induced (CID) spectra, especially for doubly charged precursors. This is in part due an insufficient understanding the characteristics and consequently a failure database search engines make use rich...
Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, global false discovery rate is used filter out positives for identifying credible peptides. However, it found that the actual level of in peptides often control and behaves differently different genomes.To quantitatively model this problem, we theoretically analyze subgroup rates annotated Our analysis shows annotation completeness ratio genome dominant factor influencing FDR...
Abstract Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification protein interactors, such as proteins, DNA, RNA carbohydrates. However, it is challenging to perform high-throughput Uaa cross-linking products due complexities samples data analysis processes. Enrichable Uaas can effectively reduce simplify analysis, but few cross-linked peptides were identified from mammalian cell with these Uaas. Here we develop an...
MS-based de novo peptide sequencing has been improved remarkably with significant development of mass-spectrometry and computational approaches but still lacks quality-control methods. Here we proposed a novel algorithm pSite to evaluate the confidence each amino acid rather than full-length peptides obtained by sequencing. A semi-supervised learning approach was used discriminate correct acids from random one; then, an expectation-maximization adaptively control false amino-acid rate (FAR)....
Here we report the discovery and identification of antibacterial substances from secondary metabolites a new strain Bacillus velezensis BA-26. The whole genome B. BA-26 was sequenced. Its data were annotated, four potentially unknown gene clusters nine known metabolite synthetic analyzed excavated by antiSMASH software. Based on predicted BA-26, material isolated purified extracellular conducted in combination with mass spectrometry data. A total 24 antifungal compounds identified, namely,...
Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to complexity spectra, majority spectra cannot be interpreted at present. The existence unexpected or unknown protein post-translational modifications a major reason. This paper describes an efficient and sequence database-independent approach detecting abundant in high-accuracy peptide spectra. based on observation that modified its unmodified counterpart are correlated with each other...
The effect of anaerobic activated sludge (AS) and granular (GS) as inoculum on methane production (MP) with different ammonia levels was compared. About 35% MP loss observed when the level exceeded 3 g NH4+ N/L in AS reactors 5 GS reactors. Propionate accumulation 66–80% lower than that ammonium concentration higher N/L. Nevertheless, lactate appeared to be an important intermediate product under a high level. impact further discussed. Under concentration, extracellular polymeric substance,...
Steady improvement in Orbitrap-based mass spectrometry (MS) technologies has greatly advanced the peptide sequencing speed and depth. In-depth analysis of performance state-of-the-art MS optimization key parameters can improve efficiency. In this study, we first systematically compared two popular data-dependent acquisition approaches, with Orbitrap as first-stage (MS1) analyzer same (high-high approach) or ion trap (high-low second-stage (MS2) analyzer, on Fusion spectrometer. High-high...
Virtual machine live migration technology, as an important support for cloud computing, has become a central issue in recent years. The virtual machines' runtime environment is migrated from the original physical server to another server, maintaining machines running at same time. Therefore, it can make load balancing among servers and ensure quality of service. However, security cannot be ignored due immature development it. This paper we analyze threats migration, compare current proposed...