Comparison of the origin and phenolic contents of Lycium ruthenicum Murr. by high‐performance liquid chromatography fingerprinting combined with quadrupole time‐of‐flight mass spectrometry and chemometrics

The fruits of Lycium ruthenicum Murr. have long been used in folk medicine. Nevertheless, detailed information related to its phenolic composition and its quality control remains scarce. In this study, a simple and reproducible method, based on high‐performance liquid chromatography combined with chemometrics, was developed to authenticate 18 samples of L. ruthenicum Murr. collected from different parts of China through fingerprint analysis. The main peaks were identified by quadrupole time‐of‐flight electrospray ionization mass spectrometry. Four phenolics were quantified, and the most abundant phenolic compound in almost all samples was kukoamine A. Hierarchical cluster analysis and principal component analysis were applied to classify these samples. Also, a total of 26 compounds, which were mainly phenolic compounds and anthocyanins, were identified or tentatively identified based on the available literature and standard references. Among these, 16 were reported for the first time in the extract. The results showed that there was no significant difference between L. ruthenicum fruits from different provinces in terms of chemical composition. Also, the fingerprint together with chemometric analyses and quadrupole time‐of‐flight electrospray ionization mass spectrometry are promising methods for evaluating the quality consistency, identification, and comprehensive evaluation of L. ruthenicum .     

Qualitative and quantitative analysis of the major constituents in Jin‐Mu‐Gan‐Mao tablet by high‐performance liquid chromatography with diode‐array detection and quadrupole time‐of‐flight tandem mass spectrometry

Jin‐Mu‐Gan‐Mao tablet is a well‐known traditional Chinese medicinal preparation, which has been used to treat the common cold in China. In this study, a systematic method was established for the qualitative and quantitative analysis of the major constituents in Jin‐Mu‐Gan‐Mao tablet. First, a method of high‐performance liquid chromatography with diode‐array detection and quadrupole time‐of‐flight mass spectrometry was developed for identification of the multi‐constituents. Thirty‐one compounds including ten phenolic acids, 18 flavonoids, and three iridoid glycosides were clearly identified by comparison with the reference standards, and 11 compounds were deduced by comparison with the literature data. Second, a new quantitative analysis method of Jin‐Mu‐Gan‐Mao tablet was established by high‐performance liquid chromatography with diode‐array detection. Twelve compounds, either with high contents or strong bioactivities, were chosen as marker components. This analytical method was validated through intra‐ and interday precision, repeatability, and stability, with respective relative standard deviations less than 1.74, 2.54, 2.44, and 2.48%. The limits of detection and quantification were less than 0.327 and 0.881 μg/mL, respectively. The overall recoveries ranged from 97.04–102.76% (relative standard deviation ≤ 2.91%). Then this validated method was applied to determine ten batches of Jin‐Mu‐Gan‐Mao tablet. The results indicated that these new approaches can be applicable for the qualitative and quantitative analysis of Jin‐Mu‐Gan‐Mao tablet.     

Chemical cross‐linking with a diazirine photoactivatable cross‐linker investigated by MALDI‐ and ESI‐MS/MS

Crystallography and nuclear magnetic resonance are well‐established methods to study protein tertiary structure and interactions. Despite their usefulness, such methods are not applicable to many protein systems. Chemical cross‐linking of proteins coupled with mass spectrometry allows low‐resolution characterization of proteins and protein complexes based on measuring distance constraints from cross‐links. In this work, we have investigated cross‐linking by means of a heterobifunctional cross‐linker containing a traditional N‐hydroxysuccinimide (NHS) ester and a UV photoactivatable diazirine group. Activation of the diazirine group yields a highly reactive carbene species, with potential to increase the number of cross‐links compared with homobifunctional, NHS‐based cross‐linkers. Cross‐linking reactions were performed on model systems such as synthetic peptides and equine myoglobin. After reduction of the disulfide bond, the formation of intra‐ and intermolecular cross‐links was identified and the peptides modified with both NHS and diazirine moieties characterized. Fragmentation of these modified peptides reveals the presence of a marker ion for intramolecular cross‐links, which facilitates identification. Copyright © 2010 John Wiley & Sons, Ltd.     

Multi‐constituent determination and fingerprint analysis of Scutellaria indica L. using ultra high performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry

An ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry method integrating multi‐constituent determination and fingerprint analysis has been established for quality assessment and control of Scutellaria indica L. The optimized method possesses the advantages of speediness, efficiency, and allows multi‐constituents determination and fingerprint analysis in one chromatographic run within 11 min. 36 compounds were detected, and 23 of them were unequivocally identified or tentatively assigned. The established fingerprint method was applied to the analysis of ten S. indica samples from different geographic locations. The quality assessment was achieved by using principal component analysis. The proposed method is useful and reliable for the characterization of multi‐constituents in a complex chemical system and the overall quality assessment of S. indica.     

Denoising and multivariate analysis of time‐of‐flight SIMS images

Time‐of‐flight SIMS (ToF‐SIMS) imaging offers a modality for simultaneously visualizing the spatial distribution of different surface species. However, the utility of ToF‐SIMS datasets may be limited by their large size, degraded mass resolution and low ion counts per pixel. Through denoising and multivariate image analysis, regions of similar chemistries may be differentiated more readily in ToF‐SIMS image data. Three established denoising algorithms—down‐binning, boxcar and wavelet filtering—were applied to ToF‐SIMS images of different surface geometries and chemistries. The effect of these filters on the performance of principal component analysis (PCA) was evaluated in terms of the capture of important chemical image features in the principal component score images, the quality of the principal component score images and the ability of the principal components to explain the chemistries responsible for the image contrast. All filtering methods were found to improve the performance of PCA for all image datasets studied by improving capture of image features and producing principal component score images of higher quality than the unfiltered ion images. The loadings for filtered and unfiltered PCA models described the regions of chemical contrast by identifying peaks defining the regions of different surface chemistry. Down‐binning the images to increase pixel size and signal was the most effective technique to improve PCA performance. Copyright © 2003 John Wiley & Sons, Ltd.     

Quantitative fingerprinting based on the limited‐ratio quantified fingerprint method for an overall quality consistency assessment and antioxidant activity determination of Lianqiao Baidu pills using HPLC with a diode array detector combined with chemometric methods

Lianqiao Baidu pills are widely used herbal medicinal preparation that were analyzed to develop a quality consistency technique. The characteristic fingerprints of 28 batches of Lianqiao Baidu pill samples were established at five wavelengths and simultaneously assessed by using a limited‐ratio quantified fingerprint method using 15 marker compounds. The principal component analysis and fingerprinting results were compared, and the qualitative classification of the samples by principal component analysis agreed with their quantitative evaluation by the limited‐ratio quantified fingerprint method. Furthermore, the antioxidant activities of the samples were surveyed and determined using a 2,2‐diphenyl‐1‐picrylhydrazyl radical‐scavenging approach. A relationship between the common peaks in the fingerprints and the antioxidant activities was established using a partial least squares model. The relationship can be used both to determine the antioxidant activities of the Lianqiao Baidu pill preparations in vitro and as a reference for the selection of active constituents for sample quality classification. The classification results for the samples based on principal component analysis agreed with the quantitative evaluation by the limited‐ratio quantified fingerprint method, which demonstrated that the method can be applied to the holistic quality control of traditional Chinese medicine and herbal preparations.     

MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry based targeted quantitative proteomics platform

Mass spectrometry (MS)‐based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS‐based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. In such approaches, synthetic reference peptides that are the stable isotope labeled version of proteotypic peptides of proteins to be quantitated are used as internal standards enabling specific identification and absolute quantification of targeted peptides. The quantification of targeted peptides is achieved using the intensity ratio of a native peptide to the corresponding reference peptide whose spike‐in amount is known. However, a manual calculation of the ratios can be time‐consuming and labor‐intensive, especially when the number of peptides to be tested is large. To establish a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (LC/MALDI TOF/TOF)‐based targeted quantitative proteomics pipeline, we have developed a software named Mass Spectrometry based Quantification (MSQ). This software can be used to automate the quantification and identification of targeted peptides/proteins by the MALDI TOF/TOF platform. MSQ was applied to the detection of a selected group of targeted peptides in pooled human cerebrospinal spinal fluid (CSF) from patients with Alzheimer's disease (AD) in comparison with age‐matched control (OC). The results for the automated quantification and identification of targeted peptides/proteins in CSF were in good agreement with results calculated manually. Copyright © 2010 John Wiley & Sons, Ltd.     

Chemical fingerprint of Ganmaoling granule by double‐wavelength ultra high performance liquid chromatography and ultra high performance liquid chromatography with quadrupole time‐of‐flight mass spectrometry

A method incorporating double‐wavelength ultra high performance liquid chromatography with quadrupole time‐of‐flight mass spectrometry was developed for the investigation of the chemical fingerprint of Ganmaoling granule. The chromatographic separations were performed on an ACQUITY UPLC HSS C₁₈ column (2.1 × 50 mm, 1.8 μm) at 30°C using gradient elution with water/formic acid (1%) and acetonitrile at a flow rate of 0.4 mL/min. A total of 11 chemical constituents of Ganmaoling granule were identified from their molecular weight, UV spectra, tandem mass spectrometry data, and retention behavior by comparing the results with those of the reference standards or literature. And 25 peaks were selected as the common peaks for fingerprint analysis to evaluate the similarities among 25 batches of Ganmaoling granule. The results of principal component analysis and orthogonal projection to latent structures discriminant analysis showed that the important chemical markers that could distinguish the different batches were revealed as 4,5‐di‐O‐caffeoylquinic acid, 3,5‐di‐O‐caffeoylquinic acid, and 4‐O‐caffeoylquinic acid. This is the first report of the ultra high performance liquid chromatography chemical fingerprint and component identification of Ganmaoling granule, which could lay a foundation for further studies of Ganmaoling granule.     

Proteomic‐based analytical approach for the characterization of glutenin subunits in durum wheat

One of the main objectives of wheat glutenin subunit (GS) analysis is the identification of protein components linked to wheat quality. The proteomic characterization of glutenin has to consider the relatively low levels of arginine and lysine residues and the close sequence similarity among the different groups of these subunits, which hinders or even prevents the identification of the GS. In this study, a proteomic approach has been applied to resolve the heterogeneity of wheat glutenin components. Proteins extracted from Triticum durum flour were first analyzed by two‐dimensional gel electrophoresis, which greatly reduced glutenin complexity. The identity of each spot was confirmed by nano liquid chromatography tandem mass spectrometry analysis of tryptic peptides. In parallel, measurements of the high mass range by matrix‐assisted laser desorption/ionization time‐of‐flight analysis allowed detection of the large tryptic peptides. Gathering all data from search engine interrogation, very high sequence coverage was obtained for high molecular weight GS, including Bx7 and By8, in agreement with the known genetic profile of durum wheat. In addition, a truncated form of By8, never detected before, was also found. Low molecular weight GS (LMW‐GS) B‐type was identified with reasonable sequence coverage, while a clear identification of LWM‐GS C‐ and D‐type was hindered by the incompleteness of the wheat DNA databases. This study represents the first comprehensive analysis of the glutenin proteome and provides a reliable method for classifying wheat varieties according to their glutenin profile. Copyright © 2009 John Wiley & Sons, Ltd.     

Potential of monitoring isotopologues by quantitative gas chromatography with time‐of‐flight mass spectrometry for metabolomic assay

Because of the extreme complexity of metabolomic samples, the effectiveness of quantitative gas chromatography with time‐of‐flight mass spectrometry depends substantially on the expansion of the linear dynamic range. Facing the existence of numerous saturated detector signals, a data processing method based on monitoring isotopologues has been developed. The monoisotopic ion kept the high mass spectrometry sensitivity, and the less abundant isotopologue ions extended the linear dynamic range. This alternative method was proved to extend the linear dynamic range to five orders of magnitude successfully and overcome the quantitative problems induced by the ion detector saturation. Finally, to validate the applicability, the method was applied to a metabolomic assay of Alzheimer's disease. Comparing with the traditional monoisotopic method, the use of monitoring isotopologues helped us to discover an additional eight metabolites with significant difference and to conduct a more reliable principal component analysis as well. The results demonstrated that monitoring isotopologues in quantitative gas chromatography with time‐of‐flight mass spectrometry could improve the authenticity of metabolomic analysis.     

Multiple analytical methods for identification and quality evaluation of Fritillariae Thunbergii Bulbus based on biological single molecules by high‐performance liquid chromatography

Quantitative analysis for biological single molecules in Fritillariae Thunbergii Bulbus and identification method by chemometrics was established by using high‐performance liquid chromatography. Amino acids, nucleosides, and nucleobases were quantitatively analyzed, and 11 peaks were selected for species identification. A Common pattern was established for chemometrics, and then similarity analysis, principal component analysis, and hierarchical cluster analysis heatmap were applied, and the results indicated that species were ideally identified from the adulterants as Fritillariae Cirrhosae Bulbus. This evaluation method was valuable for further quality control to select the characteristic components.     

Quantitative analysis of Cistanches Herba using high‐performance liquid chromatography coupled with diode array detection and high‐resolution mass spectrometry combined with chemometric methods

We aim to determine the chemical constituents of three species of Cistanches Herba using HPLC coupled with diode array detection and high‐resolution MS. Ten phenylethanoid glycosides were identified and further quantified as marker substances by HPLC coupled with diode array detection method. The separation was conducted using an Agilent TC‐C18 column with 0.1% formic acid and methanol as the mobile phases under gradient elution. The analytical method was fully validated in terms of linearity, sensitivity, precision, repeatability as well as recovery, and subsequently applied to evaluate the quality of 36 batches of Cistanche plants. The chemometric procedures (i.e., hierarchical clustering analysis and principal component analysis) were used to compare different species of Cistanches Herba, leading to successful classification of the Cistanche samples in accordance with their origins. In conclusion, this study provides a chemical basis for quality control of Cistanches Herba.     

An Isotope‐Coded Fluorogenic Cross‐Linker for High‐Performance Target Identification Based on Photoaffinity Labeling

A photoaffinity labeling (PAL)‐based method for the rapid identification of target proteins is presented in which a high‐performance chemical tag, an isotope‐coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage. The combination of PAL and heterogeneous target‐selecting techniques significantly reduces the amount of time and protein required for identification. An additional photocleavable moiety successfully accelerated proteomic analysis using cell lysate. This method is a widely applicable approach for the rapid and accurate identification of interacting proteins.     

Determination and Fingerprint Analysis of Steroidal Saponins in roots of Liriope muscari (Decne.) L. H. Bailey by ultra high performance liquid chromatography coupled with ion trap time‐of‐flight mass spectrometry

Liriope muscari (Decne.) L. H. Bailey is a well‐known traditional Chinese medicine used for treating cough and insomnia. There are few reports on the quality evaluation of this herb partly because the major steroid saponins are not readily identified by UV detectors and are not easily isolated due to the existence of many similar isomers. In this study, a qualitative and quantitative method was developed to analyze the major components in L. muscari (Decne.) L. H. Bailey roots. Sixteen components were deduced and identified primarily by the information obtained from ultra high performance liquid chromatography with ion‐trap time‐of‐flight mass spectrometry. The method demonstrated the desired specificity, linearity, stability, precision, and accuracy for simultaneous determination of 15 constituents (13 steroidal glycosides, 25(R)‐ruscogenin, and pentylbenzoate) in 26 samples from different origins. The fingerprint was established, and the evaluation was achieved using similarity analysis and principal component analysis of 15 fingerprint peaks from 26 samples by ultra high performance liquid chromatography. The results from similarity analysis were consistent with those of principal component analysis. All results suggest that the established method could be applied effectively to the determination of multi‐ingredients and fingerprint analysis of steroid saponins for quality assessment and control of L. muscari (Decne.) L. H. Bailey.     

Multifunctional Reagents for Quantitative Proteome‐Wide Analysis of Protein Modification in Human Cells and Dynamic Profiling of Protein Lipidation During Vertebrate Development

Novel multifunctional reagents were applied in combination with a lipid probe for affinity enrichment of myristoylated proteins and direct detection of lipid‐modified tryptic peptides by mass spectrometry. This method enables high‐confidence identification of the myristoylated proteome on an unprecedented scale in cell culture, and allowed the first quantitative analysis of dynamic changes in protein lipidation during vertebrate embryonic development.     

N‐ and O‐linked glycosylation site profiling of the human basic salivary proline‐rich protein 3M

In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline‐rich protein 3M, encoded by PRB3‐M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. Reversed‐phase high‐performance liquid chromatography with high‐resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N‐deglycosylation with Peptide‐N‐Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N‐ and O‐glycosylation sites. The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O‐linked to Threonine 50, and 33 different glycans N‐linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213.     

Separation with zwitterionic hydrophilic interaction liquid chromatography improves protein identification by matrix‐assisted laser desorption/ionization‐based proteomic analysis

Comprehensive proteomic analyses necessitate efficient separation of peptide mixtures for the subsequent identification of proteins by mass spectrometry (MS). However, digestion of proteins extracted from cells and tissues often yields complex peptide mixtures that confound direct comprehensive MS analysis. This study investigated a zwitterionic hydrophilic interaction liquid chromatography (ZIC‐HILIC) technique for the peptide separation step, which was verified by subsequent MS analysis. Human serum albumin (HSA) was the model protein used for this analysis. HSA was digested with trypsin and resolved by ZIC‐HILIC or conventional strong cation exchange (SCX) prior to MS analysis for peptide identification. Separation with ZIC‐HILIC significantly improved the identification of HSA peptides over SCX chromatography. Detailed analyses of the identified peptides revealed that the ZIC‐HILIC has better peptide fractionation ability. We further demonstrated that ZIC‐HILIC is useful for quantitatively surveying cell surface markers specifically expressed in undifferentiated embryonic stem cells. These results suggested the value of ZIC‐HILIC as a novel and efficient separation method for comprehensive and quantitative proteomic analyses. Copyright © 2009 John Wiley & Sons, Ltd.     

Comprehensive characterization and quantification of multiple components in Dan‐Huang‐Qu‐Yu capsule using a multivariate data processing approach based on microwave‐assisted extraction with UHPLC and Q Exactive quadrupole‐orbitrap high‐resolution mass spectrometry

Dan‐Huang‐Qu‐Yu capsule, a Chinese herbal medicine compound preparation, is widely used for chronic pelvic inflammatory disease. In this study, a rapid, selective, and sensitive microwave‐assisted extraction ultra‐high‐performance liquid chromatography‐Q Exactive quadrupole‐orbitrap high‐resolution mass spectrometry method was developed for analyzing its chemical compositions. A total of 85 compounds, including 22 flavonoids, 8 terpenoids, 5 quinones, 5 phthaleolactone, 23 organic acids, and 22 other compounds were identified from Dan‐Huang‐Qu‐Yu capsule. Among them, 35 major compounds were unambiguously detected by comparing them with reference standards and selected as quality control markers, which were simultaneously determined in Dan‐Huang‐Qu‐Yu capsule. The established method was successfully validated and applied for simultaneous determination of 35 bioactive compounds in Dan‐Huang‐Qu‐Yu capsule from ten sample batches. The quantitative data of the analytes were analyzed by principal component analysis for quality assessment of Dan‐Huang‐Qu‐Yu capsule. Six compounds (e.g., astragaloside IV, salvianolic acid B, ellagic acid, chlorogenic acid, N‐butylidenephthalide, and luteolin) were screened out and regarded as chemical markers for quality control of Dan‐Huang‐Qu‐Yu capsule. The established method has been proved to be a novel and useful tool for rapid research of Dan‐Huang‐Qu‐Yu capsule. This research will provide reference for the scientific research of traditional Chinese medicines.     

Quality assessment of crude and processed ginger by high‐performance liquid chromatography with diode array detection and mass spectrometry combined with chemometrics

A sensitive, simple, and validated high‐performance liquid chromatography with diode array detection and mass spectrometry detection method was developed for three ginger‐based traditional Chinese herbal drugs, Zingiberis Rhizoma, Zingiberis Rhizome Preparatum, and Zingiberis Rhizome Carbonisata. Chemometrics methods, such as principal component analysis, hierarchical cluster analysis, and analysis of variance, were also employed in the data analysis. The results clearly revealed significant differences among Zingiberis Rhizoma, Zingiberis Rhizome Preparatum, and Zingiberis Rhizome Carbonisata, indicating variations in their chemical compositions during the processing, which may elucidate the relationship of the thermal treatment with the change of the constituents and interpret their different clinical uses. Furthermore, the sample consistency of Zingiberis Rhizoma, Zingiberis Rhizome Preparatum, and Zingiberis Rhizome Carbonisata can also be visualized by high‐performance liquid chromatography with diode array detection and mass spectrometry analysis followed by principal component analysis/hierarchical cluster analysis. The comprehensive strategy of liquid chromatography with mass spectrometry analysis coupled with chemometrics should be useful in quality assurance for ginger‐based herbal drugs and other herbal medicines.     

Fragmentation features of intermolecular cross‐linked peptides using N‐hydroxy‐ succinimide esters by MALDI‐ and ESI‐MS/MS for use in structural proteomics

The use of mass spectrometry coupled with chemical cross‐linking of proteins has become one of the most useful tools for proteins structure and interactions studies. One of the challenges in these studies is the identification of the cross‐linked peptides. The interpretation of the MS/MS data generated in cross‐linking experiments using N‐hydroxy succinimide esters is not trivial once a new amide bond is formed allowing new fragmentation pathways, unlike linear peptides. Intermolecular cross‐linked peptides occur when two different peptides are connected by the cross‐linker and they yield information on the spatial proximity of different domains (within a protein) or proteins (within a complex). In this article, we report a detailed fragmentation study of intermolecular cross‐linked peptides, generated from a set of synthetic peptides, using both ESI and MALDI to generate the precursor ions. The fragmentation features observed here can be helpful in the interpretation and identification of cross‐linked peptides present in cross‐linking experiments and be further implemented in search engine's algorithms. Copyright © 2011 John Wiley & Sons, Ltd.