Identifications of novel host cell factors that interact with the receptor binding domain of the SARS-CoV-2 spike protein.

SARS-CoV-2 entry into host cells is facilitated by the interaction between the receptor binding domain of its spike protein (CoV2-RBD) and host cell receptor, ACE2, promoting viral membrane fusion. The virus also uses endocytic pathways for entry, but the mediating host factors remain largely unknown. It is also unknown whether mutations in the RBD of SARS-CoV-2 variants promote interactions with additional host factors to promote viral entry. Here, we used the GST pull-down approach to identify novel surface-located host factors that bind to CoV2-RBD. One of these factors, SH3BP4, regulates internalization of CoV2-RBD in an ACE2-independent, but integrin- and clathrin-dependent manner, and mediates SARS-CoV-2 pseudovirus entry, suggesting that SH3BP4 promotes viral entry via the endocytic route. Many of the identified factors, including SH3BP4, ADAM9 and TMEM2, show stronger affinity to CoV2-RBD than to RBD of the less infective SARS-CoV, suggesting SARS-CoV-2-specific utilization. We also found factors preferentially binding to the RBD of the SARS-CoV-2 Delta variant, potentially enhancing its entry. These data identify the repertoire of host cell surface factors that function in the events leading to entry of SARS-CoV-2.

Rapid authentication of red wine by MALDI-MS combined with DART-MS.

A simple, rapid and high-throughput approach was developed for authentication of red wine for the first time, by combining spectral results from matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and direct analysis in real time mass spectrometry (DART-MS). By coupling with orthogonal partial least squares discrimination analysis (OPLS-DA), this approach enabled successful classification of 535 wines from 8 countries, with the correct classification rates of 100% on the calibration set and over 90% on the validation set for almost all countries, and 26 potential characteristic markers selected. Compared to one single technique, this approach allowed detection of more compound ions, and with better fitting and predictive performances. The satisfactory differentiation results of vintages and grape varieties further verified the robustness of the approach. This study demonstrated the feasibility of combining multiple mass spectrometric techniques for wine analysis, which can be extended to other fields or to combinations of other analytical techniques.

TMED10 mediates the trafficking of insulin-like growth factor 2 along the secretory pathway for myoblast differentiation.

The insulin-like growth factor 2 (IGF2) plays critical roles in cell proliferation, migration, differentiation, and survival. Despite its importance, the molecular mechanisms mediating the trafficking of IGF2 along the secretory pathway remain unclear. Here, we utilized a Retention Using Selective Hook system to analyze molecular mechanisms that regulate the secretion of IGF2. We found that a type I transmembrane protein, TMED10, is essential for the secretion of IGF2 and for differentiation of mouse myoblast C2C12 cells. Further analyses indicate that the residues 112-140 in IGF2 are important for the secretion of IGF2 and these residues directly interact with the GOLD domain of TMED10. We then reconstituted the release of IGF2 into COPII vesicles. This assay suggests that TMED10 mediates the packaging of IGF2 into COPII vesicles to be efficiently delivered to the Golgi. Moreover, TMED10 also mediates ER export of TGN-localized cargo receptor, sortilin, which subsequently mediates TGN export of IGF2. These analyses indicate that TMED10 is critical for IGF2 secretion by directly regulating ER export and indirectly regulating TGN export of IGF2, providing insights into trafficking of IGF2 for myoblast differentiation.

Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review.

Peptide sequencing is of great significance to fundamental and applied research in the fields such as chemical, biological, medicinal and pharmaceutical sciences. With the rapid development of mass spectrometry and sequencing algorithms, de-novo peptide sequencing using tandem mass spectrometry (MS/MS) has become the main method for determining amino acid sequences of novel and unknown peptides. Advanced algorithms allow the amino acid sequence information to be accurately obtained from MS/MS spectra in short time. In this review, algorithms from exhaustive search to the state-of-art machine learning and neural network for high-throughput and automated de-novo sequencing are introduced and compared. Impacts of datasets on algorithm performance are highlighted. The current limitations and promising direction of de-novo peptide sequencing are also discussed in this review.

Advances in rapid detection of SARS-CoV-2 by mass spectrometry.

COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.

Electrospray ionization mass spectrometry with wooden tips: A review.

Electrospray ionization (ESI) is a powerful ionization technique in mass spectrometry (MS). There has been an increasing interest for the new development of ESI technique to extend its applications. ESI-MS with wooden tips (wooden-tip ESI-MS), an ESI technique invented in 2011, enabled not only new applications but also new insights into the ESI mechanism. In this review, the technical aspects of wooden-tip ESI-MS are described, the new features of wooden-tip ESI-MS for sampling and ionization of analytes are highlighted, and the important applications of wooden-tip ESI-MS in various fields in the past 10 years, including food safety, forensic investigation, environmental analysis, biomedical analysis and protein study, are summarized. The perspectives on the further development and applications of wooden-tip ESI-MS are also discussed.

Least absolute shrinkage and selection operator-based prediction of collision cross section values for ion mobility mass spectrometric analysis of lipids.

Collision cross section (CCS) values generated from ion mobility mass spectrometry (IM-MS) have commonly been employed to facilitate lipid identification. However, this is hindered by the limited available lipid standards. Recently, CCS values were predicted by means of computational calculations, though the prediction precision was generally not good and the predicted CCS values of the lipid isomers were almost identical. To address this challenge, a least absolute shrinkage and selection operator (LASSO)-based prediction method was developed for the prediction of lipids' CCS values in this study. In this method, an array of molecular descriptors were screened and optimized to reflect the subtle differences in structures among the different lipid isomers. The use of molecular descriptors together with a wealth of standard CCS values for the lipids (365 in total) significantly improved the accuracy and precision of the LASSO model. Its accuracy was externally validated with median relative errors (MREs) of <1.1% using an independent data set. This approach was demonstrated to allow differentiation of cis/trans and sn-positional isomers. The results also indicated that the LASSO-based prediction method could practically reduce false-positive identifications in IM-MS-based lipidomics.

A distinct giant coat protein complex II vesicle population in Arabidopsis thaliana.

Plants live as sessile organisms with large-scale gene duplication events and subsequent paralogue divergence during evolution. Notably, plant paralogues are expressed tissue-specifically and fine-tuned by phytohormones during various developmental processes. The coat protein complex II (COPII) is a highly conserved vesiculation machinery mediating protein transport from the endoplasmic reticulum to the Golgi apparatus in eukaryotes1. Intriguingly, Arabidopsis COPII paralogues greatly outnumber those in yeast and mammals2-6. However, the functional diversity and underlying mechanism of distinct COPII paralogues in regulating protein endoplasmic reticulum export and coping with various adverse environmental stresses are poorly understood. Here we characterize a novel population of COPII vesicles produced in response to abscisic acid, a key phytohormone regulating abiotic stress responses in plants. These hormone-induced giant COPII vesicles are regulated by an Arabidopsis-specific COPII paralogue and carry stress-related channels/transporters for alleviating stresses. This study thus provides a new mechanism underlying abscisic acid-induced stress responses via the giant COPII vesicles and answers a long-standing question on the evolutionary significance of gene duplications in Arabidopsis.

An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking.

The fidelity of protein transport in the secretory pathway relies on the accurate sorting of proteins to their correct destinations. To deepen our understanding of the underlying molecular mechanisms, it is important to develop a robust approach to systematically reveal cargo proteins that depend on specific sorting machinery to be enriched into transport vesicles. Here, we used an in vitro assay that reconstitutes packaging of human cargo proteins into vesicles to quantify cargo capture. Quantitative mass spectrometry (MS) analyses of the isolated vesicles revealed cytosolic proteins that are associated with vesicle membranes in a GTP-dependent manner. We found that two of them, FAM84B (also known as LRAT domain containing 2 or LRATD2) and PRRC1, contain proline-rich domains and regulate anterograde trafficking. Further analyses revealed that PRRC1 is recruited to endoplasmic reticulum (ER) exit sites, interacts with the inner COPII coat, and its absence increases membrane association of COPII. In addition, we uncovered cargo proteins that depend on GTP hydrolysis to be captured into vesicles. Comparing control cells with cells depleted of the cargo receptors, SURF4 or ERGIC53, we revealed specific clients of each of these two export adaptors. Our results indicate that the vesicle formation assay in combination with quantitative MS analysis is a robust and powerful tool to uncover novel factors that mediate vesicular trafficking and to uncover cargo clients of specific cellular factors.

Integrated hand-held electrochemical sensor for multicomponent detection in urine.

Electrochemical sensors have shown great advantage and application potential in point-of-care testing (POCT) related scenarios. However, some fatal problems plague its widespread utilization, which include the susceptibility of sensors to interference in real samples (e.g. pH), the contradiction between the limited objects detectable for most sensors and the requirement of multi-target analysis in most cases, and the complicated procedures in sensor preparation as well as in routine use. This paper contributed a tip-like electrochemical sensor prototype. By integrated with a commercial pipettor, it fulfilled semi-automatic assay procedure of sampling, detection and rinsing, thus saving operational time and manual work. The tip sensor owns the property of simple fabrication and is free from any modification of extra bio/chem materials. Moreover, built on multiple electrochemical signal outputs including open circuit potential, peak current and potential of specific electrochemical reaction, this work established a novel multi-component sensing strategy, wherein detection of uric acid (UA), urea and pH in urine samples was realized by using one single working electrode. The detection range for the above targets is 5.0~600 µM for UA, 4.0~8.0 for pH and 0.5~7.0 mM for urea with the detection limits (S/N = 3) of 0.05 µM for UA and 5.4 µM for urea, and the sensitivity of pH assay is 73 mV/pH. Notably, as variation of sample pH has impact on electrochemical analysis, the pH-related parameter was introduced for calibration to diminish such interference. The developed tip sensor and the novel sensing strategy may open a new window for electrochemical technology and broaden its application in POCT.

Data storage using peptide sequences.

Humankind is generating digital data at an exponential rate. These data are typically stored using electronic, magnetic or optical devices, which require large physical spaces and cannot last for a very long time. Here we report the use of peptide sequences for data storage, which can be durable and of high storage density. With the selection of suitable constitutive amino acids, designs of address codes and error-correction schemes to protect the order and integrity of the stored data, optimization of the analytical protocol and development of a software to effectively recover peptide sequences from the tandem mass spectra, we demonstrated the feasibility of this method by successfully storing and retrieving a text file and the music file Silent Night with 40 and 511 18-mer peptides respectively. This method for the first time links data storage with the peptide synthesis industry and proteomics techniques, and is expected to stimulate the development of relevant fields.

Interdomain flexibility and interfacial integrity of ß-lactamase inhibitory protein (BLIP) modulate its binding to class A ß-lactamases.

ß-Lactamase inhibitory protein (BLIP) consists of a tandem repeat of αß domains conjugated by an interdomain loop and can effectively bind and inactivate class A ß-lactamases, which are responsible for resistance of bacteria to ß-lactam antibiotics. The varied ability of BLIP to bind different ß-lactamases and the structural determinants for significant enhancement of BLIP variants with a point mutation are poorly understood. Here, we investigated the conformational dynamics of BLIP upon binding to three clinically prevalent class A ß-lactamases (TEM1, SHV1, and PC1) with dissociation constants between subnanomolar and micromolar. Hydrogen deuterium exchange mass spectrometry revealed that the flexibility of the interdomain region was significantly suppressed upon strong binding to TEM1, but was not significantly changed upon weak binding to SHV1 or PC1. E73M and K74G mutations in the interdomain region improved binding affinity toward SHV1 and PC1, respectively, showing significantly increased flexibility of the interdomain region compared to the wild-type and favorable conformational changes upon binding. In contrast, more rigidity of the interfacial loop 135-145 was observed in these BLIP mutants in both free and bound states. Consistently, molecular dynamics simulations of BLIP exhibited drastic changes in the flexibility of the loop 135-145 in all complexes. Our results indicated for the first time that higher flexibility of the interdomain linker, as well as more rigidity of the interfacial loop 135-145, could be desirable determinants for enhancing inhibition of BLIP to class A ß-lactamases. Together, these findings provide unique insights into the design of enhanced inhibitors.

Measurement of Intracellular Nitric Oxide with a Quantitative Mass Spectrometry Probe Approach.

Nitric oxide (NO) is a molecule of physiological importance, and the function of NO depends on its concentration in biological systems, particularly in cells. Concentration-based analysis of intracellular NO can provide insight into its precise role in health and disease. However, current methods for detecting intracellular NO are still inadequate for quantitative analysis. In this study, we report a quantitative mass spectrometry probe approach to measure NO levels in cells. The probe, Amlodipine (AML), comprises a Hantzsch ester group that reacts with NO to form a pyridine, Dehydro Amlodipine (DAM). Quantification of DAM by ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) allows specific measurement of intracellular NO levels. Notably, the AML/NO reaction proceeds rapidly (within 1 s), which is favorable for NO detection considering its large diffusivity and short half-life. Meanwhile, studies under simulated physiological conditions revealed that the AML response to NO is proportional and selective. The presented UPLC-MS/MS method showed high sensitivity (LLOQ = 0.24 nM) and low matrix interference (less than 15%) in DAM quantification. Furthermore, the mass spectrometry probe approach was demonstrated by enabling the measurement of endogenous and exogenous NO in cells. Hence, the quantitative UPLC-MS/MS method developed using AML as a probe is expected to be a new method for intracellular NO analysis.

Quantitative analysis of blended oils by matrix-assisted laser desorption/ionization mass spectrometry and partial least squares regression.

Quantitative labeling of oil compositions has become a trend to ensure the quality and safety of blended oils in the market. However, methods for rapid and reliable quantitation of blended oils are still not available. In this study, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was used to profile triacylglycerols in blended oils, and partial least squares regression (PLS-R) was applied to establish quantitative models based on the acquired MALDI-MS spectra. We demonstrated that this new method allowed simultaneous quantitation of multiple compositions, and provided good quantitative results of binary, ternary and quaternary blended oils, enabling good limits of detection (e.g., detectability of 1.5% olive oil in sunflower seed oil). Compared with the conventional GC-FID method, this new method could allow direct analysis of blended oils, analysis of one blended oil sample within minutes, and accurate quantitation of low-abundance oil compositions and blended oils with similar fatty acid contents.

A high-molecular weight exopolysaccharide from the Cs-HK1 fungus: Ultrasonic degradation, characterization and in vitro fecal fermentation.

This work was to examine the impact of power ultrasound (US) on the molecular properties of a high-molecular weight (MW) exopolysaccharide (EPS) from the Cs-HK1 medicinal fungus and the utilization, and prebiotic function of the US-treated EPS fractions in human fecal microflora in vitro. The US treatment caused notable reduction of intrinsic viscosity, average MW and aggregate size of EPS in water but no significant changes in the molecular structure. The US-treated EPS fractions were consumed more rapidly by the fecal microflora, resulting in a higher total level of short chain fatty acids. They also affected the relative abundance in the microflora more beneficially than the original EPS. The results suggest that power US is effective for modifying and improving the prebiotic properties of high-MW polysaccharides.

Conformational Dynamics of the Helix 10 Region as an Allosteric Site in Class A ß-Lactamase Inhibitory Binding.

ß-Lactamase inhibitory protein (BLIP) can effectively inactivate class A ß-lactamases, but with very different degrees of potency. Understanding the different roles of BLIP in class A ß-lactamases inhibition can provide insights for inhibitor design. However, this problem was poorly solved on the basis of the static structures obtained by X-ray crystallography. In this work, ion mobility mass spectrometry, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation revealed the conformational dynamics of three class A ß-lactamases with varying inhibition efficiencies by BLIP. A more extended conformation of PC1 was shown compared to those of TEM1 and SHV1. Localized dynamics differed in several important loop regions, that is, the protruding loop, H10 loop, Ω loop, and SDN loop. Upon binding with BLIP, these loops cooperatively rearranged to enhance the binding interface and to inactivate the catalytic sites. In particular, unfavorable changes in conformational dynamics were found in the protruding loop of SHV1 and PC1, showing less effective binding. Intriguingly, the single mutation on BLIP could compensate for the unfavored changes in this region, and thus exhibit enhanced inhibition toward SHV1 and PC1. Additionally, the H10 region was revealed as an important allosteric site that could modulate the inhibition of class A ß-lactamases. It was suggested that the rigid protruding loop and flexible H10 region might be determinants for the effective inhibition of TEM1. Our findings provided unique and explicit insights into the conformational dynamics of ß-lactamases and their bindings with BLIP. This work can be extended to other ß-lactamases of interest and inspire the design of novel inhibitors.

Enhancing enrichment ability of ZIF-8 mixed matrix membrane microextraction by reverse micelle strategy for analysis of multiple ionizable bioactive components in biological samples.

Recent research aimed at the design of mixed-matrix membrane (MMM) to be used for microextraction emphasized on membrane extraction phase with high surface area and porosity. This study explored the influence that surfactants have on MMM extraction efficiency for the first time. The zeolitic imidazolate framework 8-based MMM (ZIF-8-MMM) was synthesized by in situ self-assembly of ZIF-8 on the inner wall of a hollow fiber membrane with the aim of fabricating a microextraction device. By prompting the encapsulation of ionizable analytes in the polar core of reverse micelles, the presence of surfactants in extraction solvent assisted the dissolution of analytes in the fiber membrane lumen and enhanced their adsorption onto ZIF-8. Notably, hereby a microextraction method based on the novel ZIF-8-MMM-reverse micelle (ZIF-8-MMM-RM) system was developed and employed for the extraction and quantitation of two alkaloids (berberine and jatrorrhizine) and two flavonoids (wogonin and wogonoside) in biological samples. The main factors affecting microextraction performance, identity of the extraction solvent, surfactant concentration, sample solution pH and extraction time, were investigated in detail. The method showed good linearity (r2 > 0.99) and repeatability (RSD < 10%), low limits of detection (0.10-0.31 ng mL-1) and high relative recoveries (90.03-98.84%). The enrichment factor values ranged between 48.47 and 54.96. Reverse micelle formation prompted by surfactant addition was demonstrated to effectively assist the extraction of multiple ionizable analytes from biological samples, resulting in a marked improvement of ZIF-8-MMM extraction performance.

Diagnostic fragmentation-assisted mass spectral networking coupled with in silico dereplication for deep annotation of steroidal alkaloids in medicinal Fritillariae Bulbus.

Fully understanding the chemicals in an herbal medicine remains a challenging task. Molecular networking (MN) allows to organize tandem mass spectrometry (MS/MS) data in complex samples by mass spectral similarity, which yet suffers from low coverage and accuracy of compound annotation due to the size limitation of available databases and differentiation obstacle of similar chemical scaffolds. In this work, an enhanced MN-based strategy named diagnostic fragmentation-assisted molecular networking coupled with in silico dereplication (DFMN-ISD) was introduced to overcome these obstacles: the rule-based fragmentation patterns provide insights into similar chemical scaffolds, the generated in silico candidates based on metabolic reactions expand the available natural product databases, and the in silico annotation method facilitates the further dereplication of candidates by computing their fragmentation trees. As a case, this approach was applied to globally profile the steroidal alkaloids in Fritillariae bulbus, a commonly used antitussive and expectorant herbal medicine. Consequently, a total of 325 steroidal alkaloids were discovered, including 106 cis-D/E-cevanines, 142 trans-D/E-cevanines, 29 jervines, 23 veratramines, and 25 verazines. And 10 of them were confirmed by available reference standards. Approximately 70% of the putative steroidal alkaloids have never been reported in previous publications, demonstrating the benefit of DFMN-ISD approach for the comprehensive characterization of chemicals in a complex plant organism.

Quantitative Analysis of α-1-Antitrypsin Glycosylation Isoforms in HCC Patients Using LC-HCD-PRM-MS.

The change in glycosylation of serum proteins is often associated with the development of various diseases and thus can be used for diagnosis. In this study, a liquid chromatography-tandem mass spectrometry-based method is used for accurate structural analysis and quantification of site-specific glycoforms of serum α-1-antitrypsin (A1AT) in early-stage HCC and cirrhosis patients. Serum protein A1AT was purified from patient sera by immunoprecipitation with anti-A1AT antibody conjugated agarose beads, and the isolated A1AT protein was digested and analyzed by LC-MS/MS. Two tandem mass spectrometry strategies are integrated in this study: a nontargeted stepped HCD strategy for structural analysis of A1AT glycopeptides and a targeted parallel reaction monitoring (PRM) strategy for quantification of site-specific glycoforms of A1AT in HCC and cirrhosis patient sera. Accordingly, pGlyco2.0 software was used for glycopeptide identification, and Skyline software was used for glycoform quantification using the Y1 ion (peptide+GlcNAc) in MS/MS spectra. Ten site-specific glycopeptides of A1AT were identified with stepped HCD-MS/MS in patient samples, 7 of which were further quantified using HCD-PRM-MS among patient samples. We found that our strategy was able to distinguish isomers of glycopeptides where several isomers showed distinctly different patterns between cirrhosis and HCC patients. We also found that the ratio of different charge states (2+/3+) of one glycopeptide of A1AT can significantly discriminate early-stage HCC from cirrhosis with the area under the receiver operating characteristic curve AUC of 0.9. Further analysis showed that the difference may be related to the sialic acid/galactose linkage of the glycan motif.

Rapid detection of pesticides in honey by solid-phase micro-extraction coupled with electrospray ionization mass spectrometry.

Detection of pesticide residues in food samples is important for safeguarding food quality and safety. Conventional approaches for detection of pesticides in food samples typically involve labour-intensive and time-consuming sample pretreatment and chromatographic separation. In this study, solid phase micro-extraction fibres were used to rapidly extract and enrich pesticides in honey, a popular agricultural product with complex matrix, and then directly coupled with electrospray ionization mass spectrometry for qualitative and quantitative analysis. Three pesticides, ie, atrazine, benalaxyl, and pirimicarb, were investigated using the technique and their analytical performances were evaluated. The limits of detection and limits of quantitation of all the three pesticides could fulfil the cut-off values of the international standard. Linear calibration curves were constructed with good R2 coefficients, and the accuracy and precision were in acceptable ranges for all the pesticides. The analysis time is much reduced, with only minimum sample preparation and no chromatographic separation involved. The technique is simple and easy to set up, and can be extended for analysis of other analytes and sample systems.