Offline two-dimensional liquid chromatography coupled with ion mobility-quadrupole time-of-flight mass spectrometry enabling fourdimensional separation and characterization of the multicomponents from white ginseng and red ginseng

Inherent complexity of plant metabolites necessitates the use of multi-dimensional information to accomplish comprehensive profiling and confirmative identification.A dimension-enhanced strategy,by offline two-dimensional liquid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry(2 D-LC/IM-QTOF-MS)enabling four-dimensional separations(2 D-LC,IM,and MS),is proposed.In combination with in-house database-driven automated peak annotation,this strategy was utilized to characterize ginsenosides simultaneously from white ginseng(WG)and red ginseng(RG).An offline 2 DLC system configuring an Xbridge Amide column and an HSS T3 column showed orthogonality 0.76 in the resolution of ginsenosides.Ginsenoside analysis was performed by data-independent high-definition MSE(HDMSE)in the negative ESI mode on a Vion?IMS-QTOF hybrid high-resolution mass spectrometer,which could better resolve ginsenosides than MSEand directly give the CCS information.An in-house ginsenoside database recording 504 known ginsenosides and 58 reference compounds,was established to assist the identification of ginsenosides.Streamlined workflows,by applying UNIFI?to automatedly annotate the HDMSEdata,were proposed.We could separate and characterize 323 ginsenosides(including 286 from WG and 306 from RG),and 125 thereof may have not been isolated from the Panax genus.The established 2 D-LC/IM-QTOF-HDMSEapproach could also act as a magnifier to probe differentiated components between WG and RG.Compared with conventional approaches,this dimensionenhanced strategy could better resolve coeluting herbal components and more efficiently,more reliably identify the multicomponents,which,we believe,offers more possibilities for the systematic exposure and confirmative identification of plant metabolites.

Two-dimensional gel electrophoresis and surface-enhanced laser desorption ionization-time of flight-mass spectrometry for detection of protein expression profiles in the hippocampus following closed brain injury

Gene expression profile changes in brain regions following traumatic brain injury at the gene level cannot sufficiently elucidate gene expression time, expression amount, protein post-translational processing or modification. Therefore, it is necessary to quantitatively analyze the gene expression profile using proteomic techniques. In the present study, we established a rat model of closed brain injury using Marmarou＇s weight-drop device, and investigated hippocampal differential protein expression using two-dimensional gel electrophoresis and surface-enhanced laser desorption ionization-time of flight-mass spectrometry. A total of 364 protein peaks were detected on weak cation exchange-2 protein chips, including 37 differential protein peaks. 345 protein peaks were detected on immobilized metal affinity capture arrays-Cu, including 12 differential protein peaks Further examination of these differential proteins revealed that glucose-regulated protein and proteasome subunit alpha type 3 expression were significantly upregulated post-injury. These results indicate that brain injury can alter protein expression in the hippocampus, and that glucose-regulated protein and proteasome subunit alpha type 3 are closely associated with the occurrence and development of traumatic brain injury.

Analysis of proteomic differences between liquefied aftercataracts and normal lenses using two-dimensional gel electrophoresis and mass spectrometry

AIM：To analyze and identify the proteomic differences between liquefied after-cataracts and normal lenses by means of liquefied chromatography-tandem mass spectrometry（LC-MS/MS）.METHODS：Three normal lenses and three liquefied after-cataracts were exposed to depolymerizing reagents to extract the total proteins.Protein concentrations were separated using two-dimensional gel electrophoresis（2-DE）.The digitized images obtained with a GS-800 scanner were then analyzed with PDQuest7.0 software to detect the differentially-expressed protein spots.These protein spots were cut from the gel using a proteome work spot cutter and subjected to in-gel digestion with trypsin.The digested peptide separation was conducted by LC-MS/MS.RESULTS：The 2-DE maps showed that lens proteins were in a p H range of 3-10 with a relative molecular weight of21-70 kD.The relative molecular weight of the more abundant proteins was localized at 25-50 kD,and the isoelectric points were found to lie between PI 4-9.The maps also showed that the protein level within the liquefied after-cataracts was at 29 points and significantly lower than in normal lenses.The 29 points were identified by LC-MS/MS,and ten of these proteins were identified by mass spectrometry and database queries：beta-crystallin B1,glyceraldehyde-3-phosphate dehydrogenase,carbonyl reductase（NADPH）1,c DNA FLJ55253,gamma-crystallin D,GAS2-like protein 3,sorbitol dehydrogenase,DNA FLJ60282,phosphoglycerate kinase,and filensin.CONCLUSION：The level of the ten proteins may play an important role in the development of liquefied aftercataracts.

Establishing a protein expression profile database for the normal human pituitary gland using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry

In this study, we selected adult normal pituitary gland tissues from six patients during operations for pituitary microadenomas via the transsphenoidal approach for extended normal pituitary tissue resection around the tumor, and analyzed the protein expression of human normal pituitary using two-dimensional high-performance liquid chromatography combined with LTQ-Orbitrap mass spectrometry proteomics technology. The ten most highly expressed proteins in normal human pituitary were： alpha 3 type VI collagen isoform 5 precursor （abundance among tall pituitary proteins 1.30%）, fibrinogen beta chain preproprotein （0.99%）, vimentin （0.73%）, prolactin （0.69%）, ATP synthase, H~ transporting and mitochondrial F1 complex beta subunit precursor （0.52%）, keratin I （0.49%）, growth hormone （0.45%）, carbonic anhydrase I （0.40%）, heat shock protein 90 kDa I （0.31%）, and annexin V （0.30%）. Based on the biological function classifications of these proteins, the top three categories by content were neuroendocrine proteins （abundance among all pituitary proteins, 40.1%）, catalytic and metabolic proteins （28.3%）, and cell signal transduction proteins （9.8%）. Based on cell positioning classification, the top three categories were cell organelle （24.5%） membrane （20.8%）, and cytoplasm （13.0%）. Based on biological process classification, the top three categories of proteins are involved in physiological processes （42.9%）, cellular processes （40.4%）, and regulation of biological processes （9.1%）. Our experimental findings indicate that a protein expression profile database of normal human pituitary can be precisely and efficiently established by proteomics technology.

Analyzing crude oils from the Junggar Basin(NW China) using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry(GC×GC-TOFMS)

As a new technology of analyzing crude oils, comprehensive two-dimensional gas chromatography cou- pled with time-of-flight mass spectrometry （GCxGC- TOFMS） has received much research attention. Here we present a case study in the Junggar Basin of NW China. Results show that the hydrocarbons, including saturates and aromatics, were all well-separated without large co- elution, which cannot be realized by conventional one-dimensional GC-MS. The GC×GC technique is especially effective for analyzing aromatics and low-to-middle- molecular-weight hydrocarbons, such as diamondoids. The geochemical characteristics of crude oils in the study area were investigated through geochemical parameters extracted by GC×GC-TOFMS, improving upon the understanding obtained by GC-MS. Thus, the work here represents a new successful application of GC×GC- TOFMS, showing its broad usefulness in petroleum geochemistry.

Cerebrospinal fluid diagnostic markers for two-dimensional electrophoresis-mass spectrometry in Parkinson’s disease patients

BACKGROUND： Previous studies have confirmed the existence of specific proteins in body fluid of Parkinson＇s disease （PD） patients. However, the existing research has contained several interference factors with poor reproducibility and has not focused on patients grouped according to disease duration. OBJECTIVE： To verify differential expression of proteins in cerebrospinal fluid of PD patients grouped in order of disease severity through the use of two-dimensional electrophoresis-mass spectrometry methods. DESIGN, TIME AND SETTING： The proteomic-based, case-control study was performed between September 2008 and June 2009 at the Key Laboratory of Neurology in the First Affiliated Hospital of Chongqing Medical University. PARTICIPANTS： A total of 52 outpatients and/or inpatients, who were admitted to the Department of Neurology in the First Affiliated Hospital of Chongqing Medical University between 2008 and 2009, were randomized into the present study. Among them, 27 PD patients served as the PD group and were assigned to three subgroups according to modified Webster, Hoehn, and Yahr rating scales： 14 = mild, 8 = moderate, and 5 = severe; non-PD group of 16 patients included 5 cases of viral meningitis, 3 cases of acute myelitis, 1 case of Guillain-Barre syndrome, 2 cases of tuberculous meningitis, 2 cases of restless legs syndrome, and 3 cases of essential tremor; control group （n = 9） consisted of muscular tension headache in 6 cases, as well as syncope, trigeminal neuralgia, idiopathic orthostatic hypotension in 1 case. METHODS： Cerebrospinal fluid was collected from the involved patients using the lumbar puncture method. Proteins in the cerebrospinal fluid were separated by two-dimensional electrophoresis. MAIN OUTCOME MEASURES： Characteristics of protein electrophoresis patterns were analyzed, differentially expressed proteins were detected using matrix-assisted laser desorption ionization time of flight mass spectrometry, and protein data were analyzed in the Mascot database. RESULTS： Five protein electropherograms were analyzed by PDQuest 8.0, and （789 ± 32） protein spots were observed. There were significant differences in four protein spots in each of the PD sub-groups compared with the non-disease and control groups. Expression was down-regulated in three protein spots and up-regulated in one protein spot; 100% repetition rate was observed in four protein spots. According to the Mascot database, protein spots with down-regulated expression were as follows： DNA-guided RNA polymerase III subunit RPC5 （score： 50 points）; double serine, threonine, and tyrosine protein kinase （score： 64 points, P 〈 0.05）; activity-regulated cytoskeleton-associated protein （score： 58 points, P 〈 0.05）. However, G2 mitotic-specific cyclin was up-regulated （score： 84 points, P 〈 0.05）. CONCLUSION： Differential protein expression in the cerebrospinal fluid of PD patients was detected by two-dimensional electrophoresis-mass spectrometry, revealing changes in DNA-guided RNA polymerase III subunit RPC5, double serine, threonine, and tyrosine protein kinase, activity-regulated cytoskeleton-associated protein, and G2 mitotic cell cyclin, with good reproducibility.

Protein expression of sensory and motor nerves Two-dimensional gel electrophoresis and mass spectrometry

The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product （gil55628）, gfyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylgfutathione lyase, adenyfate kinase isozyme 1, two unnamed proteins products （gil55628 and gi11334163）, and poly（rC）-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.

Stepped-up development of accelerator mass spectrometry method for the detection of ^(60)Fe with the HI-13 tandem accelerator

The Moon provides a unique environment for investigating nearby astrophysical events such as supernovae.Lunar samples retain valuable information from these events,via detectable long-lived“fingerprint”radionuclides such as^(60)Fe.In this work,we stepped up the development of an accelerator mass spectrometry(AMS)method for detecting^(60)Fe using the HI-13tandem accelerator at the China Institute of Atomic Energy(CIAE).Since interferences could not be sufficiently removed solely with the existing magnetic systems of the tandem accelerator and the following Q3D magnetic spectrograph,a Wien filter with a maximum voltage of±60 kV and a maximum magnetic field of 0.3 T was installed after the accelerator magnetic systems to lower the detection background for the low abundance nuclide^(60)Fe.A 1μm thick Si_(3)N_(4) foil was installed in front of the Q3D as an energy degrader.For particle detection,a multi-anode gas ionization chamber was mounted at the center of the focal plane of the spectrograph.Finally,an^(60)Fe sample with an abundance of 1.125×10^(-10)was used to test the new AMS system.These results indicate that^(60)Fe can be clearly distinguished from the isobar^(60)Ni.The sensitivity was assessed to be better than 4.3×10^(-14)based on blank sample measurements lasting 5.8 h,and the sensitivity could,in principle,be expected to be approximately 2.5×10^(-15)when the data were accumulated for 100 h,which is feasible for future lunar sample measurements because the main contaminants were sufficiently separated.

Improved isochronous mass spectrometry with tune measurement

In conventional isochronous mass spectrometry(IMS)performed on a storage ring,the precision of mass measurements for short-lived nuclei depends on the accurate determination of the revolution times(T)of stored ions.However,the resolution of T inevitably deteriorates due to the magnetic rigidity spread of the ions,limiting the mass-resolving power.In this study,we used the betatron tunes Q(the number of betatron oscillations per revolution)of the ions and established a correlation between T and Q.From this correlation,T was transformed to correspond to a fixed Q with higher resolution.Using these transformed T values,the masses of ^(63)Ge,^(65)As,^(67)Se,and ^(71)Kr agreed well with the mass values measured using the newly developed IMS(Bρ-IMS).We also studied the systematics of Coulomb displacement energies(CDEs)and found that anomalous staggering in CDEs was eliminated using new mass values.This method of T transformation is highly effective for conventional IMS equipped with a single time-of-flight detector.

Mass Spectrometry-based Deep Coverage Proteome:Evaluation of Cellular Protein Extraction Methods

The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.

Dual mass spectrometry imaging and spatial metabolomics to investigate the metabolism and nephrotoxicity of nitidine chloride

Evaluating toxicity and decoding the underlying mechanisms of active compounds are crucial for drug development.In this study,we present an innovative,integrated approach that combines air flowassisted desorption electrospray ionization mass spectrometry imaging(AFADESI-MSI),time-of-flight secondary ion mass spectrometry(ToF-SIMS),and spatial metabolomics to comprehensively investigate the nephrotoxicity and underlying mechanisms of nitidine chloride(NC),a promising anti-tumor drug candidate.Our quantitive AFADESI-MSI analysis unveiled the region specific of accumulation of NC in the kidney,particularly within the inner cortex(IC)region,following single and repeated dose of NC.High spatial resolution ToF-SIMS analysis further allowed us to precisely map the localization of NC within the renal tubule.Employing spatial metabolomics based on AFADESI-MSI,we identified over 70 discriminating endogenous metabolites associated with chronic NC exposure.These findings suggest the renal tubule as the primary target of NC toxicity and implicate renal transporters(organic cation transporters,multidrug and toxin extrusion,and organic cation transporter 2(OCT2)),metabolic enzymes(protein arginine N-methyltransferase(PRMT)and nitric oxide synthase),mitochondria,oxidative stress,and inflammation in NC-induced nephrotoxicity.This study offers novel insights into NC-induced renal damage,representing a crucial step towards devising strategies to mitigate renal damage caused by this compound.

Bacterial Protein Profiling——Comparison of Three Mass Spectrometry Methodologies

Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.

Ultra-soft Desorption Assisted Mass Spectrometry using Picosecond Infrared Laser for the Detection of lons in the Liquid Surface

To identify the species in liquid surface using mass spectrometry,we must eliminate or reduce interferences during the vaporization or desorption of the species from the liquid surface.It is much more challenging to isolate the ionic,larger species from the liquid surface,because of the frangible structures and the higher solvation energies of those species.Here we demonstrate a new mass spectrometry in which the ionic species at the liquid surface can be desorbed with ultrasoft infrared picosecond laser pulses while the liquid surface is not breached.This laser desorption assisted mass spectrometry is not only a powerful tool to detect the fragile species but also promising to investigate vibrational energy transfer dynamics in the liquid surface.

Determination of Ten Kinds of Alpha-2 Agonists Residues in Animal Derived Food by UHPLC-Triple Quadrupole/Composite Linear Ion Trap Mass Spectrometry

[Objectives]The paper was to establish an ultra high performance liquid chromatography-quadrupole/linear ion trap complex mass spectrometry for the determination of 10 kinds ofα2-receptor agonists in animal derived food.[Methods]The samples were extracted with sodium carbonate buffer solution and ethyl acetate,and analyzed by mass spectrometry after solid phase extraction and high performance liquid chromatography separation.[Results]Ten kinds ofα2-receptor agonists showed a good linear relationship in the range of 1-100μg/mL,with the average recovery of over 69%and the relative standard deviation less than 8.32%.The detection limit of 10 kinds of α_(2)-receptor agonists was up to 1μg/kg.[Conclusions]The method has good selectivity and strong anti-interference ability,and can meet the requirements of 10 kinds ofα2-receptor agonists residues in animal derived food.

Research on the Upper Limit of Accuracy for Predicting Theoretical Tandem Mass Spectrometry

In recent years, numerous theoretical tandem mass spectrometry prediction methods have been proposed, yet a systematic study and evaluation of their theoretical accuracy limits have not been conducted. If the accuracy of current methods approaches this limit, further exploration of new prediction techniques may become redundant. Conversely, a need for more precise prediction methods or models may be indicated. In this study, we have experimentally analyzed the limits of accuracy at different numbers of ions and parameters using repeated spectral pairs and integrating various similarity metrics. Results show significant achievements in accuracy for backbone ion methods with room for improvement. In contrast, full-spectrum prediction methods exhibit greater potential relative to the theoretical accuracy limit. Additionally, findings highlight the significant impact of normalized collision energy and instrument type on prediction accuracy, underscoring the importance of considering these factors in future theoretical tandem mass spectrometry predictions.

Determination on Heavy Metals Content of Achyranthes bidentata Blume. through Inductively Coupled Plasma Mass Spectrometry (ICP-MS)

[Objective] The inductively coupled plasma mass spectrometry(ICP-MS)was constructed to determine the contents of lead,cadmium,mercury and arsenic in Archyranthes bidentata Blume.[Method]Under the optimum operation condition of ICP-MS,the samples were digested by microwave.The element 114In was taken as an internal standard element to compensate body effect and ICP-MS method was used to determine the contents of lead,cadmium,mercury and arsenic.[Result]For the determined elements,the correlation coefficient(r)of standard curve was over 0.9995 and recovery rate was from 96.7% to 106.4% while RSD was less than 11.2%.The result of determination showed that the heavy metal content in Archyranthes bidentata Blume.beyond standard was serious.[Conclusion]The constructed ICP-MS method with simple operation,rapid response,accuracy and high sensitivity in this experiment could be used for quality control of Chinese medicinal materials by detecting heavy metal contents in different Chinese medicinal materials from original places.

Photoionization Mass Spectrometric and Kinetic Modeling of Low-pressure Pyrolysis of Benzene

Pyrolysis of benzene at 30 Torr was studied from 1360 K to 1820 K in this work. Synchrotron vacuum ultraviolet photoionization mass spectrometry was employed to detect the pyroly- sis products such as radicals, isomers and polycyclic aromatic hydrocarbons, and measure their mole fraction profiles versus temperature. A low-pressure pyrolysis model of benzene was developed and validated by the experimental results. Rate of production analysis was performed to reveal the major reaction networks in both fuel decomposition and aromatic growth processes. It is concluded that benzene is mainly decomposed via H-abstraction reaction to produce phenyl and partly decomposed via unimolecular decomposition reac- tions to produce propargyl or phenyl. The decomposition process stops at the formation of acetylene and polyyne species like diacetylene and 1,3,5-hexatriyne due to their high thermal stabilities. Besides, the aromatic growth process in the low-pressure pyrolysis of benzene is concluded to initiate from benzene and phenyl, and is controlled by the even carbon growth mechanism due to the inhibited formation of C5 and C7 species which play important roles in the odd carbon growth mechanism.

Separation of Ions from Volatile Organic Compounds Using High-Field Asymmetric Waveform Ion Mobility Spectrometry-Mass Spectrometer

A combination of high-field asymmetric waveform ion mobility spectrometry （FAIMS） with mass spectrometer （MS） was analyzed. FAIMS separates ions from the volatile organic compounds in the gas-phase as an ion-filter for MS. The sample ions were created at ambient pressure by ion source, which was equipped with a 10.6 eV UV discharge lamp （A=116.5 nm）. The drift tube of FAIMS is composed of two parallel planar electrodes and the dimension is 10 mm×8 mm×0.5 mm. FAIMS was investigated when driven by the high-filed rectangular asymmetric waveform with the peak-to-peak voltage of 1.36 kV at the frequency of 1 MHz and the duty cycle of 30%. The acetone, the butanone, and their mixture were adopted to characterize the FAIMS-MS. The mass spectra obtained from MS illustrate that there are ion-molecular reactions between the ions and the sample neutral molecular. And the proton transfer behavior in the mixture of the acetone and the butanone is also observed. With the compensation voltage tuned from -30 V to 10 V with a step size of 0.1 V, the ion pre-separation before MS is realized.

High Performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometric Analysis of Bilobalide and Ginkgolides in Ginkgo biloba L. Leaves

The ginkgo terpenoids including bilobalide and ginkgolides are the main pharmaceutical components in the leaves or extracts of Ginkgo biloba L. In this paper, the analysis of bilobalide and ginkgolides in leaves of Ginkgo biloba L. by high performance liquid chromatography (HPLC)-electrospray ionization (ESI)-mass spectrometry (MS) was carried out. The separation was performed on Inertsil ODS3 column with methanol-water (36:64) as mobile phase, with 1 mL·min -1 of flow rate at 35℃. Then the mass spectrum analysis was conducted by ZMD micromass electrospray ionization (ESI)-mass spectrometer (MS). The HPLC total ion chromatogram and selected ion chromatogram (with 325, 407, 423, 439 of m/z) of the sample and ESI-/MS mass spectra of the peaks in the chromatograms were obtained. So bilobalide, ginkgolide A, B, C and J in Ginkgo biloba L. leaves were identified. The method is easy and rapid, with a good accuracy.