ORCID Profile
0000-0002-6233-8459
Current Organisation
Fudan University
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Publisher: American Chemical Society (ACS)
Date: 10-11-2017
DOI: 10.1021/ACS.ANALCHEM.7B03820
Abstract: Bacterial typing is of great importance in clinical diagnosis, environmental monitoring, food safety analysis, and biological research. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is now widely used to analyze bacterial s les. Identification of bacteria at the species level can be realized by matching the mass spectra of s les against a library of mass spectra of known bacteria. Nevertheless, in order to reasonably type bacteria, identification accuracy should be further improved. Herein, we propose a new framework to the identification and assessment for MALDI-MS based bacterial analysis. Our approach combines new measures for spectra similarity and a novel bootstrapping assessment. We tested our approach on a general data set containing the mass spectra of 1741 strains of bacteria and another challenging data set containing 250 strains, including 40 strains in the Bacillus cereus group that were previously claimed to be impossible to resolve by MALDI-MS. With the bootstrapping assessment, we achieved much more reliable predictions at both the genus and species level, and enabled to resolve the Bacillus cereus group. To the best of the authors' knowledge, our method is the first to provide a statistical assessment to MALDI-MS based bacterial typing that could lead to more reliable bacterial typing.
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.ACA.2016.11.021
Abstract: Mass spectrometry (MS)-based proteome profiling is essential for molecular diagnostics in modern biomedical study. To date, s le preparation including protein extraction and proteolysis is still very challenging and lack of efficiency. Recently tips-based s le preparation protocols exhibit strong potentials to achieve the goal of "a proteome in an hour". However, in-tip proteolysis is still rarely reported and far from ideal for dealing with complex bio-s les. In this work, nanoreactors encapsulated micropipette tips were demonstrated as high performance devices for fast (∼minutes) and multiplexing proteolysis to assist the profiling of cancer cells proteome. Nanoporous silica materials with controlled pore size and surface chemistry were prepared as nanoreactors and encapsulated in micropipette tips for efficient in situ proteolysis. The as-constructed device showed desirable sensitivity (LOD of 0.204 ± 0.008 ng/μL and LOQ of 0.937 ± 0.055 ng/μL), selectivity, stability (two months under -20 °C), reusability (at least 10 times), and little memory effect in MS based bottom-up proteomic analysis. It was used for comprehensive protein mapping from cancer cell lines. The number of identified proteins was increased by 18%, 22%, 52%, and 52% dealing with HepG2, F56, MCF7, and HCCLM3 cancer cells, compared to traditional in-solution proteolysis based bottom-up proteomic strategy. With the enhanced performance, our work built a novel, efficient and miniaturized platform for facile proteomic s le preparation, which is promising for advanced biomarkers discovery in biomedical study.
Publisher: Royal Society of Chemistry (RSC)
Date: 2018
DOI: 10.1039/C7SE00591A
Abstract: The influence of structural parameters of highly-ordered silicon nanowire arrays on their solar-driven HER performance is systematically investigated.
Publisher: Royal Society of Chemistry (RSC)
Date: 2011
DOI: 10.1039/C1MB05140G
Abstract: Tryptic digestion of proteins in trypsin loaded porous silica has been shown to be highly efficient. Enzymatic silica-reactors were prepared by immobilizing trypsin into macroporous ordered siliceous foam (MOSF) and into mesoporous SBA-15 silica which has a smaller pore size. The tryptic products from the silica reactors were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and a higher proteolysis efficiency was obtained with MOSF. These results can be well interpreted by a sequential digestion model taking into account the confinement and concentration enrichment of both the substrates and enzymes within the silica pores. Proteins at low concentrations and proteins in urea and surfactant solutions were also successfully digested with the MOSF-based reactor and identified by MS. Considering that the immobilized trypsin could retain its enzymatic activity for weeks, this MOSF reactor provides many advantages compared to free enzyme proteolysis. As a proof-of-concept, the digest of a real complex s le extracted from the cytoplasm of mouse liver tissue using trypsin loaded MOSF yielded better results than the typical in-solution protocol.
Publisher: Elsevier BV
Date: 2020
Publisher: Springer Science and Business Media LLC
Date: 09-01-2020
DOI: 10.1038/S41467-019-13866-Z
Abstract: Data-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of s les. However, s le-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA analysis, which is time-consuming and limits the identification/quantification by DIA to the peptides identified by DDA. Herein, we propose DeepDIA, a deep learning-based approach to generate in silico spectral libraries for DIA analysis. We demonstrate that the quality of in silico libraries predicted by instrument-specific models using DeepDIA is comparable to that of experimental libraries, and outperforms libraries generated by global models. With peptide detectability prediction, in silico libraries can be built directly from protein sequence databases. We further illustrate that DeepDIA can break through the limitation of DDA on peptide rotein detection, and enhance DIA analysis on human serum s les compared to the state-of-the-art protocol using a DDA library. We expect this work expanding the toolbox for DIA proteomics.
Publisher: Wiley
Date: 09-10-2013
Abstract: Amino-functionalized macroporous silica foam (NH2 -MOSF) has been developed as a host reactor to realize highly efficient proteolysis in acidic solutions where normal tryptic reactions cannot occur. The digestion protocol consists simply of adding the functionalized NH2 -MOSF into the protein and trypsin solutions without altering the bulk pH or preloading the enzymes on the materials. With this protocol, digestion of s le fractions from LC can be efficiently realized in the acidic solutions directly. Digestion of a protein fraction extracted from rat liver tissue after LC separation was performed to illustrate this principle, where 103 proteins were successfully identified at pH 3 after 1.5 h of tryptic digestion.
Publisher: Wiley
Date: 23-02-2009
Abstract: Enriching peptides: Novel TiO(2)-modified macroporous materials (Ti-MOSF, see figure) have been synthesized with high surface area, large pore volume, and functional surfaces that are rich in coordinatively unsaturated Ti(IV) species, which can be applied in the specific extraction of phosphopeptides and which show a preferential capture of multi-phosphorylated peptides with low detection limits and high selectivity.
Publisher: American Chemical Society (ACS)
Date: 09-08-2018
DOI: 10.1021/ACS.ANALCHEM.8B02258
Abstract: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now widely used to characterize bacterial s les for clinical diagnosis, food safety control, environmental monitoring, and so on. However, existing standard approaches are only applied to analyze single colonies purified by plate culture, which limits the approaches to cultivable bacteria and makes the whole approaches time-consuming. In this work, we propose a new framework to analyze MALDI-TOF spectra of bacterial mixtures and to directly characterize each component without purification procedures. The framework is a combination of a synthetic mixture model based on a non-negative linear combination of candidate reference spectra and a statistical assessment by in silico generated spectra via a jackknife res ling. Ninety-seven model bacterial mixture s les and 8 cocultured blind-coded bacterial mixture s les, containing up to 6 strains in varied ratios in each s le, together with a reference database containing the mass spectra of 1081 strains, were used to validate the framework. High sensitivity (>80%, with error rate 60% for balanced quaternary and pentabasic mixtures, and 48%-71% for asymmetric situation, with error rate <5%. The work can facilitate rapid and reliable characterization of bacterial mixtures without purification procedures, which is of practical value in clinical diagnosis, food safety control, environmental monitoring, and so on. The framework can be further applied to many other spectroscopy-based analytics to interpret spectra from mixed s les.
Publisher: American Chemical Society (ACS)
Date: 12-06-2009
DOI: 10.1021/AC900550Q
Abstract: A novel nanopore based digestion strategy has been developed by directly adding a macroporous material as catalyst to the conventional in-solution reaction system. Without increasing the enzyme or protein concentrations, this simple digestion approach exhibits high proteolysis efficiency and selectivity due to the in situ fast adsorption of both enzymes and proteins from bulk solution into the macropores of the catalysts, where the target substrates and enzymes are greatly concentrated and confined in the nanospace to realize a quick digestion. Based on the electrostatic interaction matching between the biomolecules and catalysts, selective extraction and digestion of proteins with different isoelectric points can be achieved by adjusting the surface charge of the catalysts. This nanoporous reaction system has been successfully applied to the analysis of a complex biological s le, where 293 proteins are identified, while only 100 proteins are obtained by the standard overnight in-solution digestion. The present nanospace confined digestion strategy will lead to promising advances not only in proteomics but also in other applications where enzymatic reactions are involved.
Publisher: Royal Society of Chemistry (RSC)
Date: 19-08-2014
DOI: 10.1039/C4CC05545D
Abstract: Lysozyme can be electrochemically detected after adsorption at an electrified gel-water interface. Ex situ characterization by electrostatic spray ionization mass spectrometry provides insights into the interfacial detection mechanism by allowing changes to the tertiary structure of electroadsorbed lysozyme to be fingerprinted for the first time.
No related grants have been discovered for Liang Qiao.