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Proteomic analysis plays an important role in basic biological studies and precision medicine. However, real samples contain numerous proteins with a wide dynamic distribution range. Such high complexity of the samples has a drastic effect on the identification coverage of proteins. Consequently, with advancements in mass spectrometry (MS) technology, concomitant improvements in separation technologies for simplifying the sample should be critical. With the advantages of small sample loading volume, high separation efficiency, and high speed, capillary electrophoresis (CE) coupled to MS has been gained much attention in the field of proteomics research. A nanoflow sheath liquid interface and a sheathless interface have been developed and commercialized, boosting the development of the CE-MS technology. Capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), and capillary electrochromatography (CEC) have been successfully combined with MS, and CZE-MS has widespread application. In proteomic research, the "bottom-up" strategy, which is based on the separation and identification of enzymatic peptides, is widely applied. With the limit of detection as low as 1 zmol for peptides, CE-MS has been successfully applied to single-cell proteomic analysis. Besides, CE is complementary to reversed-phase liquid chromatography (RPLC), providing a new approach for the separation and identification of peptides with similar hydrophobic properties (especially, post-translational peptides). The "top-down" strategy, which is based on the separation and identification of intact proteins, can directly provide more accurate and complete information about proteins. For protein separation, CE is advantageous in terms of the high separation resolution and high protein recovery, thereby improving the sensitivity and coverage of protein identification. Native MS enables successful identification and characterization of protein complexes under nondenaturing conditions. Because of the good compatibility of CE with MS, attempts have been made to use CE coupled with native MS for the separation and identification of protein complexes. In this review, the development of the CE-MS technology is first reported, including a robust and sensitive CE-MS interface, and a separation mode coupled to MS. Then, the application of the CE-MS technology to "bottom-up", "top-down" and native MS analysis is discussed. The superiority of CE-MS in proteomic analysis is also emphasized. Finally, the promising future prospects of CE-MS are discussed.

A novel method of the simultaneous detection of multiple kinds of allergenic proteins in infant food with parallel reaction monitoring (PRM) mode using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was established. In this method, unique peptides with good stability and high sensibility were used to quantify the corresponding allergenic proteins. Furthermore, multiple kinds of allergenic proteins are inspected simultaneously with high sensitivity. In addition, such method was successfully used for the detection of multiple allergenic proteins in infant food. As for the sample preparation for infant food, compared with the traditional acetone precipitation strategy, the protein extraction efficiency and capacity of resisting disturbance are both higher with in-situ filter-aided sample pretreatment (i-FASP) method. All allergenic proteins gave a good linear response with the correlation coefficients ( R 2 ) ≥ 0.99, and the largest concentration range of the allergenic proteins could be four orders of magnitude, and the lowest detection limit was 0.028 mg/L, which was better than that reported in references. Finally, the method was conveniently used to detect the allergens from four imported infant food real samples. All the results demonstrate that this novel strategy is of great significance for providing a rapid and reliable analytical technique for allergen proteomics.

Isotopic labeling and isobaric labeling are two kinds of the typical quantification method that have been widely used in proteomics analysis. Herein, a novel quantitative strategy, partially isobaric peptide termini labeling (PITL), was developed to overcome the drawbacks of each above-mentioned labeling strategy, by simultaneously collecting the quantitative information from both MS and MS/MS spectrum. PITL is based on the site-selective N-terminus dimethylation labeling of peptide α-N-termini and the free ε-amino group of lysines, resulting in the partially isobaric labeling of peptides. The relative quantification can then be achieved by comparing the intensities of precursor ions in MS spectra and a, b and y ions in MS/MS spectra. The quantitative analysis of differently labeled yeast digests pooled with various ratios indicated the good quantitative accuracy, reproducibility, coverage and wide dynamic range of PITL strategy. Furthermore, PITL was applied to the quantitative proteome analysis of two mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates (Hca-F and Hca-P). Given its low cost, simple operation and good accuracy, PITL might have great potential in the quantitative proteome analysis of biological samples., Biological Significance: The partially isobaric peptide termini labeling (PITL) method enabled to simultaneously obtain the quantitative information from MS and MS/MS spectrum, which combined the advantages of these two strategies. Relative quantification could be achieved by comparing the intensities of parent ions in MS spectra and a, b, y ions in the MS/MS spectra. The quantitative analysis for differently labeled yeast digests mixed at various ratios indicated the good accuracy, reproducibility, quantitative coverage and wide dynamic range of the PITL strategy. Finally, we found 84 differentially expressed proteins in mouse hepatocarcinoma ascites syngeneic cell lines with low and high lymph node metastasis rates with PITL strategy and 77 proteins of them were consistently quantified in our previous studies., (Copyright © 2014 Elsevier B.V. All rights reserved.)

New types of imidazolium-based iodoacetamide tags were designed, synthesized and further exploited for cysteinyl-peptide analysis with superior labeling efficiency, high stability, improved ionization efficiency, and increased charge states by mass spectrometry. For the first time, the effects of these kinds of tags on the mass spectrometry performance of the derivatized peptides were investigated, which is of great importance to help us design more efficient tags for the analysis of peptides or proteins, especially for those with low abundance.

The cationic reagent 1-(3-aminopropyl)-3-butylimidazolium bromide (BAPI) was exploited for the derivatization of carboxyl groups on peptides. Nearly 100% derivatization efficiency was achieved with the synthetic peptide RVYVHPI (RI-7). Furthermore, the peptide derivative was stable in a 0.1% TFA/water solution or a 0.1% (v/v) TFA/acetonitrile/water solution for at least one week. The effect of BAPI derivatization on the ionization of the peptide RI-7 was further investigated, and the detection sensitivity was improved >42-fold via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), thus outperforming the commercial piperazine derivatization approach. Moreover, the charge states of the peptide were largely increased via BAPI derivatization by electrospray ionization (ESI) MS. The results indicate the potential merits of BAPI derivatization for high sensitivity peptide analysis by MS.

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Proteomics is one of the core contents of life science in the post-genomic era, among which it is very important to develop the analytical techniques with high resolution, high sensitivity, high accuracy and high throughput. With the advantages of facile preparation, fast mass transfer, low backpressure and easy modification, monolithic materials have been widely used in proteomic analysis. This review summarizes the preparation methods of different kinds of monolithic materials (including organic polymer monoliths, silica-based monoliths, organic-inorganic hybrid silica monoliths) and their applications in proteomic study such as the digestion of proteins, the separation of proteins or peptides, high throughput analysis integrating online digestion, separation and identification.

A novel method for the separation and detection of low molecular weight (LMW) acids was developed using monolithic immobilized pH gradient-based capillary isoelectric focusing coupled with mass spectrometry. Two main parameters, focusing conditions and delivery buffer conditions, which might affect separation efficiency, were optimized with the focusing time of 7 min at 350 V/cm and the delivery buffer of 50% (v/v) acetonitrile in 10 mmol/L ammonium formate (pH 3.0). Under these conditions, the linear correlation between the volume of delivery solvent and the pK(a) of the model components was observed. In addition, the separation mechanism of LMW acids was proposed as well. We suppose that this method may provide a useful tool for the characterization of LMW components (e.g. natural organic matter of different origins)., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A novel on-line system combining supercritical fluid extraction (SFE) and two-dimensional high performance liquid chromatography (2D-HPLC) was developed. A trap column and two three-port valves were employed to couple SFE and 2D-HPLC system, which was composed of a CN column and a monolithic silica column, connected by a 10-port dual-position valve. The analytes extracted by supercritical CO2 were completely transferred to the 2D-HPLC system. After separation in two orthogonal modes, the eluents were delivered to APCI-tandem-MS for identification of the samples. In this way, sample preparation, separation, detection, and identification were integrated into an on-line system permitting analysis of the fruiting bodies of Ganoderma lucidum, and at least 73 components in the extract were resolved with calculated peak capacity of up to 1643.

A comprehensive two-dimensional liquid chromatographic (2D-LC) separation system based on the combination of a CN column and a Merck Chromolith Flash reversed-phase column was developed for the separation of components in Adinandra nitida, one type of traditional Chinese medicine (TCM). The two dimensions were connected by a ten-port, dual-position valve controlled automatically by software written in-house. The effluents were detected by both ultraviolet and atmospheric pressure chemical ionization source ion trap tandem mass spectrometry (MS). The calculated peak capacity of the 2D-LC-MS/MS system was above 1240. More than 57 components were resolved in the methanol extract from Adinandra nitida leaves, and five of these were identified based on their relative retention times, molecular weights and MS/MS spectra.

Tissue kallikrein, generally existing in living bodies as prokallikrein, is a serine proteinase that has proven of great significance to treat hypertension, cardiopathy and nephropathy. Although the extraction of tissue kallikrein from human urine is the most commonly used method to obtain such a protein, not only the yield is very little, but also the procedure is rather complex. Furthermore, the biological safety is uncertain. Therefore, the preparation of such a protein by genetic engineering method, including gene expression, cell culture, separation and purification, is very important. In this paper, a new method to obtain purified tissue prokallikrein excreted from insect cells by liquid chromatography has been proposed. In contrast to the previously published papers, the purification procedure is simplified to only three steps with the final yield of 57% and the purity of 95%, which is not only convenient, but also low-cost and suitable for the large-scale preparation of such a protein. The purified protein is further validated as prokallikrein by high performance liquid chromatography-mass spectrometry and amino acid sequencing.

Cross-linkers play a critical role in capturing protein dynamics in chemical cross-linking mass spectrometry techniques. Various types of cross-linkers with different backbone features are widely used in the study of proteins. However, it is still not clear how the cross-linkers' backbone affect their own structure and their interactions with proteins. In this study, we systematically characterized and compared methylene backbone and polyethylene glycol (PEG) backbone cross-linkers in terms of capturing protein structure and dynamics. The results indicate the cross-linker with PEG backbone have a better ability to capture the inter-domain dynamics of calmodulin, adenylate kinase, maltodextrin binding protein and dual-specificity protein phosphatase. We further conducted quantum chemical calculations and all-atom molecular dynamics simulations to analyze thermodynamic and kinetic properties of PEG backbone and methylene backbone cross-linkers. Solution nuclear magnetic resonance was employed to validate the interaction interface between proteins and cross-linkers. Our findings suggest that the polarity distribution of PEG backbone enhances the accessibility of the cross-linker to the protein surface, facilitating the capture of sites located in dynamic regions. By comprehensively benchmarking with disuccinimidyl suberate (DSS)/bis-sulfosuccinimidyl-suberate(BS3), bis-succinimidyl-(PEG)2 revealed superior advantages in protein dynamic conformation analysis in vitro and in vivo , enabling the capture of a greater number of cross-linking sites and better modeling of protein dynamics. Furthermore, our study provides valuable guidance for the development and application of PEG backbone cross-linkers. [ABSTRACT FROM AUTHOR]

Protein dynamics play a crucial role in their diverse functions. The intracellular environment significantly influences protein dynamics, particularly for intrinsically disordered proteins (IDPs). To comprehensively capture structural information from various proteins within cells and characterize protein dynamics, chemical cross‐linking mass spectrometry was employed. In this study, we introduce a hierarchical decoding strategy that enables the investigation of protein dynamics in vivo. Computational analysis based on distance restraints derived from cross‐links is used to infer protein dynamics in cells. To facilitate this analysis, we leverage the prior structure obtained from AlphaFold2. By employing this strategy, we can characterize the full‐length structure of multi‐domain proteins taking into account their distinct dynamic features. Furthermore, by combining restraint sampling with an unbiased sampling and evaluation approach, we can provide a comprehensive description of the intrinsic motion of IDPs. Consequently, the hierarchical strategy we propose holds significant potential in advancing our understanding of the molecular mechanisms that undelie protein functions in cells. [ABSTRACT FROM AUTHOR]

Chemical cross‐linking mass spectrometry (CXMS) has emerged as a powerful technology to analyze protein complexes. However, the progress of in vivo CXMS studies has been limited by cross‐linking biocompatibility and data analysis. Herein, a glycosidic bond‐based MS‐cleavable cross‐linker of trehalose disuccinimidyl ester (TDS) was designed and synthesized, which was fragmented in MS under CID/HCD to simplify the cross‐linked peptides into conventional single peptides via selective cleavage between glycosidic and peptide bonds under individual MS collision energy. Consequently, the cross‐linking identification accuracy and throughput were significantly enhanced, and the popular MS mode of stepped HCD was allowed. In addition, TDS showed proper cell‐penetrating properties while being highly water‐soluble, making it non‐DMSO dependent during solubilization. Collectively, TDS provides a promising toolkit for CXMS characterization of living systems with high biocompatibility and accuracy. [ABSTRACT FROM AUTHOR]

Motivation Chemical cross-linking combined with mass spectrometry (CXMS) is now a well-established method for profiling existing protein–protein interactions (PPIs) with partially known structures. It is expected to map the results of CXMS with existing structure databases to study the protein dynamic profile in the structure analysis. However, currently available structure-based analysis software suffers from the difficulty of achieving large-scale analysis. Besides, it is infeasible for structure analysis and data mining on a large scale, since of lacking global measurement of dynamic structure mapping results. Results ComMap (protein complex structure mapping) is a software designed to perform large-scale structure-based mapping by integrating CXMS data with existing structures. It allows complete the distance calculation of PPIs with existing structures in batch within minutes and provides scores for different PPI-structure pairs of testable hypothetical structural dynamism via a global view. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

• TiO 2 -based photocatalytic derivatization reaction for primary amines was developed. • Reaction was introduced into LMJSS system for rapid online derivatization in 5 s. • Derivatization enhanced the MS signals of primary amines by 5–300 fold. • Reaction was selective to alpha-unsubstituted primary amines rather than amino acids. • Method was applied to in-situ MS of neurotransmitters and drugs in mice cerebrum. In in-situ mass spectrometry (MS), different on-tissue derivatization methods have been developed to enhance the signals of poorly ionizable primary amines. However, those chemical derivatization methods are laborious and time-consuming, and are usually limited to detection of high-abundance amino acids which suppress the reaction of low-abundance monoamine neurotransmitters and drugs. Herein, A rapid and selective photocatalytic derivatization technique for alpha-unsubstituted primary amine was developed with 5-hydroxyindole as derivatization reagent and TiO 2 as photocatalyst, and was introduced into liquid microjunction surface sampling (LMJSS)-MS system as online derivatization. The results showed that the photocatalytic derivatization method largely enhanced the signals of primary amines by 5–300 fold, and were selective to alpha-unsubstituted primary amines. Thus, the suppression effects from high-abundance amino acids to the reaction of monoamine neurotransmitters and benzylamine drugs proved to be largely reduced in the new method (matrix effect>50%) comparing with those in chemical derivatization method (matrix effect<10%). In addition, the optimal pH of the derivatization reaction was measured to be 7, which indicates the mild and physiologically compatible reaction conditions. By in-situ synthesis of TiO 2 monolith in the transfer capillary of the LMJSS-MS system, rapid on-line photocatalytic derivatization was achieved and completed in 5 s during the transfer of sampling extract from the flow-probe to the MS inlet. With the new photocatalytic reactive LMJSS-MS method, detection limits of three primary amines on glass slides were in the range of 0.031–0.17 ng/mm2 with acceptable linearity (r =0.9815–0.9998) and relatively high repeatability (relative standard deviations <22.1%). Finally, endogenous tyramine, serotonin, two dipeptides and one doped benzylamine drug were identified and in-situ analyzed in the mouse cerebrum by the new method with largely enhanced signals comparing with LMJSS-MS without online derivatization. The new method provides a more selective, rapid and automated way to analyze alpha-unsubstituted amine metabolites and drugs in-situ comparing with traditional methods. [ABSTRACT FROM AUTHOR]

Due to the important roles of N-glycoproteins in various biological processes, the global N-glycoproteome analysis has been paid much attention. However, by current strategies for N-glycoproteome profiling, peptides with glycosylated Asn at N-terminus (PGANs), generated by protease digestion, could hardly be identified, due to the poor deglycosylation capacity by enzymes. However, theoretically, PGANs occupy 10% of N-glycopeptides in the typical tryptic digests. Therefore, in this study, we developed a novel strategy to identify PGANs by releasing N-glycans through the N-terminal site-selective succinylation assisted enzymatic deglycosylation. The obtained PGANs information is beneficial to not only achieve the deep coverage analysis of glycoproteomes, but also discover the new biological functions of such modification. [ABSTRACT FROM AUTHOR]

Selective enrichment and isolation of glycopeptides from complex biological samples was indispensable for mass spectrometry (MS)-based glycoproteomics, however, it remained a great challenge due to the low abundance of glycoproteins and the ion suppression of non-glycopeptides. In this work, 4-mercaptophenylboronic acid functionalized graphene oxide composites were synthesized via loading gold nanoparticles on polyethylenimine modified graphene oxide surface, followed by 4-mercaptophenylboronic acid immobilization by the formation of Au–S bonding (denoted as GO/PEI/Au/4-MPB composites). The composites showed highly specific and efficient capture of glycopeptides due to their excellent hydrophilicity and abundant boronic acid groups. The composites could selectively capture the glycopeptides from the mixture of glycopeptides and nonglycopeptides, even when the amounts of non-glycopeptides were 100 times more than glycopeptides. Compared with commercial meta -amino phenylboronic acid agarose, the composites showed better selectivity when the sample was decreased to 10 ng. These results clearly verified that the GO/PEI/Au/4-MPB composites might be a promising material for glycoproteomics analysis. [ABSTRACT FROM AUTHOR]

Abstract: An integrated platform with the combination of proteins and peptides separation was established via the unit of on-line proteins digestion, by which proteins were in sequence separated by column switch recycling size exclusion chromatography (csrSEC), on-line digested by an immobilized trypsin microreactor, trapped and desalted by two parallel C8 precolumns, separated by μRPLC with the linear gradient of organic modifier concentration, and identified by ESI-MS/MS. A 6-protein mixture, with Mr ranging from 10kDa to 80kDa, was used to evaluate the performance of the integrated platform, and all proteins were identified with sequence coverage over 5.67%. Our experimental results demonstrate that such an integrated platform is of advantages such as good time compatibility, high peak capacity, and facile automation, which might be a promising approach for proteome study. [Copyright &y& Elsevier]

Pressurized capillary electrochromatography (pCEC) was coupled with electrospray ionization mass spectrometry (ESI-MS) using a coaxial sheath liquid interface. It was used for separation and analysis of peptides and proteins. The effects of organic modifier and applied voltage on separation were investigated, and the effects of pH value of the mobile phase and the concentration of the electrolyte on ESI-MS signal were investigated. The resolution and detection sensitivity with different separation methods (pCEC, capillary high-performance liquid chromatography) coupled on-line with mass spectrometry were compared for the separation of a peptide mixture. To evaluate the feasibility and reliability of the experimental setup of the system, tryptic digests of cytochrome c and modified protein as real samples were analyzed by using pCEC- ESI-MS. [ABSTRACT FROM AUTHOR]

Many endogenous antioxidants, including glutathione (GSH), cysteine (Cys), cysteinyl-glycine (Cys-Gly) and homocysteine (Hcy) possess free thiol functional groups. In most cases, matrix-assisted laser desorption ionization (MALDI) analyses of trace amounts of thiol compounds are challenging because of their instability and poor ionization properties. We present a mass spectrometry imaging (MSI) approach for mapping of thiol compounds on brain tissue sections. Our derivatization reagents 1-(2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl)-2,4,6-trimethylpyridinium (MTMP) and 1-(2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl)-2,4,5-triphenylpyridinium (MTPP) facilitate the covalent charge-tagging of molecules containing free thiol group for the selective and rapid detection of GSH synthesis and metabolic pathway related metabolites by MALDI-MSI. The developed thiol-specific mass spectrometry imaging method realizes the quantitative detection of exogenous N-acetylcysteine tissue sections, and the detection limit in mass spectrometry imaging could reach 0.05 ng. We illustrate the capabilities of the developed method to mapping of thiol compounds on brain tissue from the chronic social defeat stress (CSDS) depression model mice. [Display omitted] • Development of pyrylium-based charged thiol labeling reagents. • Development of rapid mass spectrometry imaging methods for in-situ thiol compounds. • In situ mapping and quantification of thiol compounds on tissues. • Simultaneous imaging of GSH and thiol metabolites in mice brain. [ABSTRACT FROM AUTHOR]

Abstract A novel kind of macro-mesoporous organosilica monolith, with not only bridged-ethylene groups incorporated into the skeleton but also terminal-vinyl groups protruded from the pore-wall, was prepared so that high-loaded double bonds were achieved. Via highly efficient "thiol-ene" click reaction of such high-loaded double bonds, the surface coverage of C18 groups on monolith could be 5.54 μmol m−2, significantly larger than that of the reported separation materials, beneficial to improvement of separation resolution, especially for peptide separation. The separation performance was evaluated using alkylbenzenes and standard peptides. Furthermore, the tryptic digests of complex sample was successfully analyzed. Because of high separation resolution of our prepared hybrid monolith, the peak capacity for 6-h gradient was achieved as 482. Coupling to LTQ Orbitrap Velos Mass Spectrometry, 22523 tryptic peptides from 4423 proteins were identified from the HeLa cells, more than that using the other long-gradient separation by the same system reported, showing great promising of such monolith for large-scale in-depth proteomic analysis. Graphical abstract Image 1 Highlights • A hybrid monolith with bridged-ethylene and terminal-vinyl was prepared. • The monolith has high surface coverage of C18 groups with 5.54 μmol m−2. • Peptides were separated with high resolution and high peak capacity. • Complex sample were separated and identified by MS successfully. [ABSTRACT FROM AUTHOR]

Ubiquitination is a reversible post-translational modification that plays a pivotal role in numerous biological processes. Antibody-based approaches, as the most used methods for identifying ubiquitination sites, exist sequence recognition bias, high cost, and ubiquitin-like protein modification interference, limiting their widespread application. Here, we proposed an Antibody-Free approach for Ubiquitination Profiling, termed AFUP, by selectively clicking the ubiquitinated lysine to enrich and profile endogenous ubiquitinated peptides using mass spectrometry. Briefly, protein amines were blocked with formaldehyde, and then the ubiquitin molecules were hydrolyzed from the ubiquitinated proteins by non-specific deubiquitinases USP2 and USP21 to release the free ε-amine of lysine. Peptides containing free ε-amines were selectively enriched with streptavidin beads upon NHS-SS-biotin labeling. Finally, the enriched peptides were eluted by DTT and analyzed by LC-MS/MS, resulting in ubiquitination profiling. Preliminary experiment showed that 349 ± 7 ubiquitination sites were identified in 0.8 mg HeLa lysates with excellent reproducibility (CV = 2%) and high quantitative stability (Pearson, r ≥ 0.91) using our method. With the combination of AFUP and simple basic C18 pre-fractionation, approximately 4000 ubiquitination sites were identified in a single run of 293T cells. In addition, we showed that 209 ubiquitination sites were significantly regulated in UBE2O knockdown cells after normalized to protein abundance. In conclusion, our results demonstrated that AFUP is a robust alternative strategy for ubiquitomics research. [Display omitted] • An antibody-free approach for endogenous ubiquitination profiling was proposed. • The enrichment of ubiquitinated peptides was achieved by selectively clicking the ubiquitinated lysine ε-amine using cleavable biotinylation reagent. • A substate dataset regulated by UBE2O was built by AFUP strategy. [ABSTRACT FROM AUTHOR]

Tianzhi granule (TZG) is a traditional Chinese formula that is widely used for the treatment of vascular dementia (VaD). To discover the herbs in TZG possessing acetylcholinesterase (AChE) inhibitory activity and to screen the anti-acetylcholinesterase ingredients from active herbs. In vitro AChE inhibitory activity assay of eleven herbal extracts was conducted. An ultrafiltration combined with ultra-performance liquid chromatography-mass spectrometry method was established to screen and identify the anti-acetylcholinesterase ingredients from active extracts. In addition, in vitro AChE inhibitory activity assay and molecular docking were adopted for further investigation. Moreover, ultra-performance liquid chromatography-mass spectrometry was performed for the content determination of active compounds in TZG. Three herbs in TZG showed significant AChE inhibitory activity. A total of thirteen active ingredients were screened out and identified, and all of these compounds were present in TZG. Five available commercial standards presented moderate AChE inhibitory activity, and all of which have a relatively high content in TZG. A number of herbs and compounds with acetylcholinesterase inhibitory activity were found in TZG, which provided a scientific basis for the material basis and quality control research of TZG. [Display omitted] • An efficient strategy was applied to discover and validate active ingredients of TZG. • 13 potential active ingredients against AChE have been successfully screened out. • The inhibitory activities of five available commercial standards were validated. • Our study provided a scientific basis for improving the quality standard of TZG. [ABSTRACT FROM AUTHOR]

Cysteine-rich peptides (CRPs) are stable molecules that contain multiple disulphide bonds. Various CRPs are found in plants and animals, representing potential compounds for drug development with diverse activities. Modification of CRPs, such as glycation, has attracted increased attention due to its special structural and functional properties. Hence, this study explored a CRP isolated from the Chinese herb Achyranthes bidentata Blume, which contains a glycation modification. Herein, a reverse phase high-performance liquid chromatography system with mobile phases was used to extract and purify the peptide. The eluted peptide was detected using high resolution mass spectrometry and structurally identified using high resolution mass spectrometry and nuclear magnetic resonance. The effect of the peptide on the viability of N -methyl-D-aspartic acid (NMDA)-induced HT22 cells was determined using a cell assay. Here, a new cysteine-rich glycation peptide, termed glycation-bidentatide (Gly-BTP), with three pairs of disulphide bonds and a glycation modification at the N-terminus linked to cysteine, was discovered. Cell bioactivity assay results suggested that Gly-BTP might be a potential therapeutic and provide a neuroprotective effect in NMDA-induced HT22 murine hippocampal neuronal cells. The discovery of Gly-BTP will promote the understanding of the role of CRPs in neuroprotection. [Display omitted] • The Glycation-Bidentatide (Gly-BTP) only exist in dry root rather than fresh plants, indicating that preservation or process might be the source of Gly-BTP generation. • The native CRP is not only exist in Achyranthes bidentata Blume, but also can have chemically modified CRPs at the N-terminal and linked to cysteine. • The Gly-BTP could be a potential therapeutic and provide neuroprotection effects on N -methyl-D-aspartic acid (NMDA)-induced HT22 murine hippocampal neuronal cells. [ABSTRACT FROM AUTHOR]

Abstract: Chemical derivatization is a very promising technique for improving analysis of peptides by mass spectrometry (MS). Thereinto, development of novel tags compatible with MS and/or MS/MS has always been the focus point of study. In this review, the recent reported tags for derivatization of thiol groups of cysteine, carboxyl groups, and amino groups on peptides as well as peptides with post-translational modifications (PTMs) are summarized. Moreover, the tags used for derivatization of glycans or oligosaccharides released from glycoproteins are also reviewed. [Copyright &y& Elsevier]

Abstract: The enrichment of low abundance phosphopeptides before MS analysis is a critical step for in-depth phosphoproteome research. In this study, mesoporous titanium dioxide (TiO2) aerogel was prepared by precipitation and supercritical drying. The specific surface area up to 490.7m2 g−1 is achieved by TiO2 aerogel, much higher than those obtained by commercial TiO2 nanoparticles and by the latest reported mesoporous TiO2 spheres. Due to the large specific surface area and the mesoporous structure of the aerogel, the binding capacity for phosphopeptides is six times higher than that of conventional TiO2 microparticles (173 vs 28μmolg−1). Because of the good compatibility of enrichment procedure with MALDI-TOF-MS and the large binding capacity of TiO2 aerogel, a detection limit as low as 30amol for analyzing phosphopeptides in β-casein digest was achieved. TiO2 aerogel was further applied to enrich phosphopeptides from rat liver mitochondria, and 266 unique phosphopeptides with 340 phosphorylation sites, corresponding to 216 phosphoprotein groups, were identified by triplicate nanoRPLC-ESI-MS/MS runs, with false-positive rate less than 1% at the peptide level. These results demonstrate that TiO2 aerogel is a kind of promising material for sample pretreatment in the large-scale phosphoproteome study. [Copyright &y& Elsevier]

Abstract: A formic acid (FA)-assisted sample preparation method was presented for protein identification via mass spectrometry (MS). Detailedly, an aqueous solution containing 2% FA and dithiothreitol was selected to perform protein denaturation, aspartic acid (D) sites cleavage and disulfide linkages reduction simultaneously at 108°C for 2h. Subsequently, FA wiped off via vacuum concentration. Finally, iodoacetamide (IAA) alkylation and trypsin digestion could be performed ordinally. A series of model proteins (BSA, β-lactoglobulin and apo-Transferrin) were treated respectively using such method, followed by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The identified peptide number was increased by ∼80% in comparison with the conventional urea-assisted sample preparation method. Moreover, BSA identification was achieved efficiently down to femtomole (25±0 sequence coverage and 16±1 peptides) via such method. In contrast, there were not peptides identified confidently via the urea-assisted method before desalination via the C18 zip tip. The absence of urea in this sample preparation method was an advantage for the more favorable digestion and MALDI-TOF MS analysis. The performances of two methods for the real sample (rat liver proteome) were also compared, followed by a nanoflow reversed-phase liquid chromatography with electrospray ionization tandem mass spectrometry system analysis. As a result, 1335±43 peptides were identified confidently (false discovery rate <1%) via FA-assisted method, corresponding to 295±12 proteins (of top match=1 and requiring 2 unique peptides at least). In contrast, there were only 1107±16 peptides (corresponding to 231±10 proteins) obtained from the conventional urea-assisted method. It was serving as a more efficient protein sample preparation method for researching specific proteomes better, and providing assistance to develop other proteomics analysis methods, such as, peptide quantitative analysis. [Copyright &y& Elsevier]

Abstract: Deer antlers mature rapidly in 60 days, and subsequently shed in 5 days with rapid ossification. During this procedure, the function of deer antlers changes significantly. Therefore, the profiling of antler proteome is helpful to discover important growing and shedding regulation proteins, which might be of great significance for studying development and regeneration. In this study, a parallel protein extraction strategy was developed to extract proteins from antlers of red deer with five different lysis solutions, followed by shotgun proteomic analysis by microflow reversed-phase liquid chromatography/electrospray ionization/tandem mass spectrometry (μRPLC–ESI-MS/MS) with a 30cm-long serially coupled microcolumn. Our experimental results showed that the identified proteins extracted by five kinds of lysis solution were complementary to each other. In total, 416 unique proteins were identified, with relative molecular masses from 2000 to 600,000, and isoelectric points from 3.84 to 11.57. All these results demonstrate that the combination of parallel protein extraction strategy and μRPLC–ESI-MS/MS analysis with serially coupled long microcolumns might be of great significance for comprehensive proteomic research of deer antler. [ABSTRACT FROM AUTHOR]

Proteins carry out numerous biological functions in living cells and form a dynamic system under various physiological and pathological conditions. Advances in proteome quantitation strategies have deepened our understanding of complex biological processes. Herein, we highlight stable isotope labeling-based quantitation methods and discuss the properties of each method, directed by the features of quantitation ions. Furthermore, the applications of these methods in quantifying a variety of protein properties, including post-translational modifications, subcellular localization, turnover rate, secretion and variation in multicellular environments, are also summarized. • Stable isotope labeling-based methods for proteome quantitation. • Advantages and weaknesses of quantitation methods classified by quantitation ions. • Applications of stable isotope labeling-based methods for quantifying multiple protein properties. [ABSTRACT FROM AUTHOR]