X-Hitting: an algorithm for novelty detection and dereplication by UV spectra of complex mixtures of natural products

A major challenge in lead discovery is to detect well-known and trivial compounds rapidly, a process known as dereplication, so that isolation, structure elucidation, and pharmacological investigations can be focused on novel compounds. In this paper, we present a new algorithm, X-hitting, based on cross sample comparison of full UV spectra from HPLC analysis of highly complex natural product extracts/samples. X-Hitting allows automatic identification of known compounds but more important also allows finding of potentially new or similar compounds. We demonstrate this new algorithm by automatic identification of known structures, a task we call cross-hitting, and tentative identification of potentially new bioactive compounds, a task we call new-hitting, in HPLC data from analysis of fungal extracts. Both tasks are illustrated using 18 important reference compounds and complex fungal extracts obtained from isolates in the IBT Culture Collection held at BioCentrum-DTU, Technical University of Denmark. The receiver operating characteristics statistic is used to evaluate the performance of the compound predictor, and it was found that compounds could be identified with high confidence (AUC approximately 0.98). Based on high confidence in retrieving identical spectra, the method is extended to include similar but still different spectra.     

GC-MS/MS同位素内标法测定肉制品中N-二甲基亚硝胺

采用同位素内标定量,建立一种快速、准确测定各种肉制品N-二甲基亚硝胺的GC-MS/MS法。样品中加入D6-N-二甲基亚硝胺内标,经水蒸气蒸馏、二氯甲烷提取、分离、浓缩,用多反应监测模式(MRM)进样分析。色谱柱为HP-Innowax毛细管柱(30 m×0.32 mm,0.25μm),氦气为载气,氮气为碰撞气,流量为1.4 m L/min。结果表明:该方法检测范围在10~300 ng/m L内,线性关系良好y=77.16x-500.16(r2=0.999 6),精密度RSD为2.36%;回收率为82.9%~99.5%,检出限0.2μg/kg。对4种不同来源的肉制品共40批次进行检测,检出13批次,但均未超过限量(3μg/kg)。该方法灵敏、简便、准确、重复性好,可作为肉制品中N-二甲基亚硝胺检测的好方法。     

Analysis of perchlorate in water by reversed-phase LC/ESI-MS/MS using an internal standard technique

A new method was developed for the analysis of perchlorate in water by using reversed-phase liquid chromatograhy/electrospray ionization-mass spectrometry/mass spectrometry (LC/ESI-MS/MS) in the negative ESI mode. Selective and sensitive perchlorate detection was obtained by monitoring the 35ClO4- --> 35ClO3- and 37ClO4- --> 37ClO3- mass transitions. The 35ClO4- --> 35ClO3- transition was quantitated against the internal standard oxygen-labeled sodium perchlorate (NaCl18O4). Sample pretreatment for the removal of major common anions and dissolved metal ions along with internal standard quantitation sufficiently compensated for ion suppression caused by the matrix. The 37ClO4- --> 37ClO3- transition was examined to provide additional specificity. The method sensitivity, accuracy, and precision were investigated by analyzing fortified blank samples, field samples, and performance evaluation samples. The results (1.01-13.5 microg/L) for the proficiency evaluation samples differed from the certified values (1.04-14.1 microg/L) by 3-18%. The developed reversed-phase LC/ESI-MS/MS method was rapid, accurate, and reproducible. The calculated method detection limits were 0.007 microg/L for deionized reagent water and 0.009 microg/L for synthesized reagent water, respectively. The minimum reporting limit was conservatively set to 0.05 microg/L.     

MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products

ESI (electrospray ionization) MS and tandem mass spectrometry (MS/MS) were used for the analysis of single nucleotide polymorphisms (SNPs) and more complex genetic variations. Double-stranded (ds) PCR products were studied. PCR products of the proline [5'-x(G17)-x(C38)x-3'] and arginine variants [(5'-x(Gl7)-x(G38)x-3'] of the p53 gene are distinguished by an SNP (cytosine or guanine) and were discriminated using both quadrupole and quadrupole ion trap MS analysis. A 69 bp arginine mutant PCR product [5'-x(C17)-x(G38)x-3'] with a negating switch has the same mass as the proline variant but was readily distinguishable on ion trap MS/MS analysis; fragments containing the mutation site, but not the polymorphism, were identified. The 69 bp PCR products were restriction-enzyme-digested, to create 43 bp fragments. ESI quadrupole ion trap MS/MS analysis of the 43 bp product-ion spectra readily demonstrated both polymorphism and negating switch sites. MS and MS/MS are powerful and complementary techniques for analysis of DNA. MS can readily distinguish SNPs but MS/MS is required to differentiate isomeric PCR products (same nucleotide composition but different sequence).     

Molecular criteria for discriminating adipose fat and milk from different species by NanoESI MS and MS/MS of their triacylglycerols: application to archaeological remains

A new multistep analytical methodology is described in this paper for the precise identification of triacylglycerols, which are biomarkers of dairy products and subcutaneous fats, that may be chemically identified in archaeological pottery. It consists of the analysis of the total lipid extract from different kinds of fats by high-temperature gas chromatography, performed in order to select the ceramic vessels in which animal fats are well preserved, followed by nanoelectrospray QqTOF mass spectrometry that allows for distinguishing the specific origins of the lipids detected (namely, cow, sheep, or goat). The analysis of model samples, cow and goat dairy products and cow and sheep adipose fats, was successfully achieved. The fatty acid composition of each triacylglycerol was identified, which allowed for the discrimination of subcutaneous fats and dairy fats and distinguishing between cow and goat milk. This methodology was then applied to archaeological samples, and the presence of goat milk, cow milk, and possibly sheep subcutaneous fat was assessed based on the discriminating criteria found on modern fats.     

超高效液相色谱质谱法测定水产品中恩诺沙星含量的不确定度评价

采用超高效液相色谱质谱法测定水产品中恩诺沙星的含量,分析不确定度的来源,建立评估的数学模型,通过计算不确定度的各主要分量,给出了测定结果的扩展不确定度.评定结果表明:影响检测结果不确定度的主要因素为标准溶液的配置、样品的回收率和测量重复性等.     

Trace analysis of antidepressant pharmaceuticals and their select degradates in aquatic matrixes by LC/ESI/MS/MS

Treated wastewater effluent is a potential environmental point source for antidepressant pharmaceuticals. A quantitative method was developed for the determination of trace levels of antidepressants in environmental aquatic matrixes using solid-phase extraction coupled with liquid chromatography-electrospray ionization tandem mass spectrometry. Recoveries of parent antidepressants from matrix spiking experiments for the individual antidepressants ranged from 72 to 118% at low concentrations (0.5 ng/L) and 70 to 118% at high concentrations (100 ng/L) for the solid-phase extraction method. Method detection limits for the individual antidepressant compounds ranged from 0.19 to 0.45 ng/L. The method was applied to wastewater effluent and samples collected from a wastewater-dominated stream. Venlafaxine was the predominant antidepressant observed in wastewater and river water samples. Individual antidepressant concentrations found in the wastewater effluent ranged from 3 (duloxetine) to 2190 ng/L (venlafaxine), whereas individual concentrations in the waste-dominated stream ranged from 0.72 (norfluoxetine) to 1310 ng/L (venlafaxine).     

LC/MS/MS analyses of an oleander extract for cancer treatment

An HPLC/MS/MS method has been developed for the characterization and quantification of the cardiac glycosides oleandrin, odoroside, neritaloside and the aglycone oleandrigenin, all contained in a patented-hot-water extract of Nerium oleander L (Anvirzel). Qualitative analysis of such extracts was achieved using a hybrid tandem quadrupole time-of-flight (QqTOF) mass spectrometer. Collision-induced dissociation (CID) mass spectra of oleandrin, oleandrigenin, odoroside, and neritaloside were obtained with greater than 5 ppm mass accuracy and resolution routinely in excess of 8000 (fwhm). The detection limit for oleandrin of 20 pg (injected) was realized when the precursor-to-product ion transition, m/z 577 --> 373, was monitored. We have also applied the analytical method to the determination of oleandrin, oleandrigenin, neritaloside, and odoroside in human plasma following an intramuscular injection of Anvirzel.     

Coumarin tags for improved analysis of peptides by MALDI-TOF MS and MS/MS. 1. Enhancement in MALDI MS signal intensities

The goal of this study was the development of N-terminal tags to improve peptide identification using high-throughput MALDI-TOF MS and MS/MS. The proposed tags, commercially available fluorescent derivatives of coumarin, can be advantageous for peptide analysis in both MS and MS/MS modes. This paper, part 1, will focus on the influence of derivatization on the intensities of MALDI-TOF MS signals of peptides. Labeling peptides with tags containing the coumarin core was found to enhance the intensities of peptide peaks (in some cases over 40-fold) in MALDI-TOF MS using CHCA and 2,5-DHAP matrixes. The signal enhancement was found to be peptide- and matrix-dependent, being the most pronounced for hydrophilic peptides. No correlation was found between the UV absorptivity of the tags at the excitation wavelengths typical for UV-MALDI and the magnitude of the signal enhancement. Interestingly, peptides labeled with Alexa Fluor 350, a coumarin derivative containing a sulfo group (i.e., bearing strong negative charge), showed a 5-15-fold increase in intensity of MALDI MS signal in the positive ion mode, relative to the underivatized peptides, when 2,5-DHAP was used as the matrix. The Alexa Fluor 350 tag yielded a significantly higher signal relative to that for the CAF tag, likely due to the increased hydrophobicity of the coumarin structure. With 2,5-DHB, a decrease of MALDI MS signal was observed for all coumarin-labeled peptides, again relative to the unlabeled species. These findings support the hypothesis that derivatization with coumarin, a relatively hydrophobic structure, improves incorporation of hydrophilic peptides into hydrophobic MALDI matrixes, such as CHCA and 2,5-DHAP.     

Coumarin tags for analysis of peptides by MALDI-TOF MS and MS/MS. 2. Alexa Fluor 350 tag for increased peptide and protein Identification by LC-MALDI-TOF/TOF MS

The goal of this study was the development of N-terminal tags to improve peptide identification using high-throughput MALDI-TOF/TOF MS. Part 1 of the study was focused on the influence of derivatization on the intensities of MALDI-TOF MS signals of peptides. In part 2, various derivatization approaches for the improvement of peptide fragmentation efficiency in MALDI-TOF/TOF MS are explored. We demonstrate that permanent cation tags, while significantly improving signal intensity in the MS mode, lead to severe suppression of MS/MS fragmentation, making these tags unsuitable for high-throughput MALDI-TOF/TOF MS analysis. In the present work, it was found that labeling with Alexa Fluor 350, a coumarin tag containing a sulfo group, along with guanidation of epsilon-amino groups of Lys, could enhance unimolecular fragmentation of peptides with the formation of a high-intensity y-ion series, while the peptide intensities in the MS mode were not severely affected. LC-MALDI-TOF/TOF MS analysis of tryptic peptides from the SCX fractions of an E. coli lysate revealed improved peptide scores, a doubling of the total number of peptides, and a 30% increase in the number of proteins identified, as a result of labeling. Furthermore, by combining the data from native and labeled samples, confidence in correct identification was increased, as many proteins were identified by different peptides in the native and labeled data sets. Additionally, derivatization was found not to impair chromatographic behavior of peptides. All these factors suggest that labeling with Alexa Fluor 350 is a promising approach to the high-throughput LC-MALDI-TOF/TOF MS analysis of proteomic samples.     

Accelerated solvent extraction followed by on-line solid-phase extraction coupled to ion trap LC/MS/MS for analysis of benzalkonium chlorides in sediment samples

Benzalkonium chlorides (BACs) were successfully extracted from sediment samples using a new methodology based on accelerated solvent extraction (ASE) followed by an on-line cleanup step. The BACs were detected by liquid chromatography/ion trap mass spectrometry (LC/MS) or tandem mass spectrometry (MS/MS) using an electrospray interface operated in the positive ion mode. This methodology combines the high efficiency of extraction provided by a pressurized fluid and the high sensitivity offered by the ion trap MS/MS. The effects of solvent type and ASE operational variables, such as temperature and pressure, were evaluated. After optimization, a mixture of acetonitrile/water (6:4 or 7:3) was found to be most efficient for extracting BACs from the sediment samples. Extraction recoveries ranged from 95 to 105% for C12 and C14 homologues, respectively. Total method recoveries from fortified sediment samples, using a cleanup step followed byASE, were 85% for C12BAC and 79% for C14BAC. The methodology developed in this work provides detection limits in the subnanogram per gram range. Concentrations of BAC homologues ranged from 22 to 206 microg/kg in sediment samples from different river sites downstream from wastewater treatment plants. The high affinity of BACs for soil suggests that BACs preferentially concentrate in sediment rather than in water.     

Application of stored waveform ion modulation 2D-FTICR MS/MS to the analysis of complex mixtures

Component identification of complex mixtures, whether they are from polymeric formulations or combinatorial synthesis, by conventional MS/MS techniques generally requires component separation by chromatography or mass spectrometry. An automated means of acquiring simultaneous MS/MS data from a complex mixture without prior separation is obtained from stored waveform ion modulation (SWIM) two-dimensional FTICR MS/MS. The technique applies a series of SWIFT excitation waveforms whose frequency domain magnitude spectrum is a sinusoid increasing in frequency from one waveform to the next. The controlled dissociation of the precursor ions produces an associated modulation of the product ion abundances. Fourier transformation of these abundances reveals the encoded modulation frequency from which connectivities of precursor and product ions are observed. The final result is total assignment of product ions for each precursor ion in a mixture from one automated experiment. We demonstrated the applicability of SWIM 2D-FTICR MS/MS to two diverse samples of industrial importance. We characterized structured polyester oligomers and products derived from combinatorial synthesis. Fragmentation pathways identified in standard serial ion isolation MS/MS experiments were observed for trimethylolpropane/methyl hexahydrophthalic anhydride. A 20-component sample derived from combinatorial synthesis was fragmented, and the template ion along with another key fragment ion was identified for each of the 20 components.     

Simultaneous analysis of multiple classes of antibiotics by ion trap LC/MS/MS for assessing surface water and groundwater contamination

Solid-phase extraction (SPE) and liquid chromatography in combination with ion trap mass spectrometry (LC/MS/MS) conditions were optimized for the simultaneous analysis of 13 antibiotics belonging to multiple classes and caffeine in 3 different water matrixes. The single-cartridge extraction step was developed using a reversed-phase cartridge, resulting in recoveries for the 14 compounds ranging from 71 to 119% with relative standard deviations of 16% or lower. The analytes were separated in one chromatographic run, and the SPE-LC/MS/MS detection limits ranged from 0.03 to 0.19 microg/L. The SPE procedure was validated in groundwater, surface water, and wastewater. The analysis of samples from each of the three water matrixes revealed clindamycin (1.1 microg/L) in surface water and multiple antibiotics in wastewater (0.10-1.3 microg/L). The use of identification points to unambiguously assign the identity of antibiotics in various water matrixes was applied to an ion trap data-dependent scanning method, which simultaneously collects full scan and full scan MS/MS data for the unequivocal identification of target analytes.     

In vivo deamidation characterization of monoclonal antibody by LC/MS/MS

The spontaneous nonenzymatic deamidation of glutaminyl and asparaginyl residues of peptides and proteins has been observed both in vitro and in vivo. Deamidation may change the structure and function of a peptide or protein, potentially resulting in decreased bioactivity, as well as alterations in pharmacokinetics and antigenicity of the protein pharmaceutical. Therefore, it is necessary to monitor the effect of storage and formulation conditions on deamidation of a protein drug candidate. Of particular interest is the investigation of in vivo deamidation mechanisms of protein drug candidates. Several methods are available to characterize the deamidation of peptides and proteins. We present here a LC/MS/MS method used to evaluate the deamidation of an antibody after in vivo administration. A humanized monoclonal IgG1 antibody (MAb) has several "hot spots" for spontaneous deamidation. One site, amino acid residue Asn55 located in the CDR2 region of the heavy chain, is of particular interest since deamidation at this site greatly decreases the binding activity. MAb was administered to cynomolgus monkeys by intravenous and subcutaneous routes. At various times after dosing, monkey serum was prepared and MAb captured by the immobilized antigen or a goat anti-human IgG Fcgamma antibody. The captured MAb was treated with trypsin followed by endoproteinase Glu-C. The digests were separated on RP-HPLC and analyzed by MS/MS on Q-Tof Global mass spectrometer. Using this method, we were able to determine the deamidation half-life of amino acid residue Asn55 in vivo and the ratio of the deamidated derivatives, i.e., isoAsp55 and Asp55. The method is rapid and sensitive with low-nanogram quantities of protein detected in the biological matrix.     

Enhanced characterization of complex proteomic samples using LC-MALDI MS/MS: exclusion of redundant peptides from MS/MS analysis in replicate runs

Due to the complexity of proteome samples, only a portion of peptides and thus proteins can be identified in a single LC-MS/MS analysis in current shotgun proteomics methodologies. It has been shown that replicate runs can be used to improve the comprehensiveness of the proteome analysis; however, high-intensity peptides tend to be analyzed repeatedly in different runs, thus reducing the chance of identifying low-intensity peptides. In contrast to commonly used online ESI-MS, offline MALDI decouples the separation from MS acquisition, thus allowing in-depth selection for specific precursor ions. Accordingly, we extended a strategy for offline LC-MALDI MS/MS analysis using a precursor ion exclusion list consisting of all identified peptides in preceding runs. The exclusion list eliminated redundant MS/MS acquisitions in subsequent runs, thus reducing MALDI sample depletion and allowing identification of a larger number of peptide identifications in the cumulative dataset. In the analysis of the digest of an Escherichia coli lysate, the exclusion list strategy resulted in a 25% increase in the number of unique peptide identifications in the second run, in contrast to simply pooling MS/MS data from two replicate runs. To reduce the increased LC analysis time for repeat runs, a four-column multiplexed LC system was developed to carry out separation simultaneously. The multiplexed LC-MALDI MS provides a high-throughput platform to utilize the exclusion list strategy in proteome analysis.     

Pinpointing biomarkers in proteomic LC/MS data by moving-window discriminant analysis

The identification of differential patterns in data originating from combined measurement techniques such as LC/MS is pivotal to proteomics. Although "shotgun proteomics" has been employed successfully to this end, this method also has severe drawbacks, because of its dependence on largely untargeted MS/MS sequencing and databases for statistical analyses. Alternatively, several MS-signal-based (MS/MS-independent) methods have been published that are mainly based on (univariate) Student's t-tests. Here, we present a more robust multivariate alternative employing linear discriminant analysis. Like the t-test-based methods, it is applied directly to LC/MS data, instead of using MS/MS measurements. We demonstrate the method on a number of simulated data sets, as well as on a spike-in LC/MS data set, and show its superior performance over t-tests.     

Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain

It remains an open question as to whether experiments involving collision-induced dissociation (CID) can provide a viable approach for monitoring spatially resolved deuteration levels in electrosprayed polypeptide ions. A number of laboratories reported the successful application of CID following solution-phase H/D exchange (HDX), whereas others found that H/D scrambling precluded site-specific measurements. The aim of the current work is to help clarify the general feasibility of HDX-CID methods, using a 22-residue zinc-bound protein domain (Zn-ZBD) as model system. Metal binding in Zn-ZBD should confer structural rigidity, and the presence of several basic residues should sequester mobile charge carriers in the gas phase. Both of these factors were expected to suppress the extent of scrambling. HDX was carried out by employing rapid on-line mixing, thereby mimicking conditions typically encountered in kinetic pulse-labeling studies. Quadrupole time-of-flight MS/MS of pulse-labeled Zn-ZBD provides high sequence coverage. However, the measured fragment deuteration levels do not correlate with the known H-bonding pattern of Zn-ZBD, suggesting the occurrence of extensive scrambling. Instead of showing a uniform distribution, the fragment ions reveal a distinct nonrandom pattern of deuteration levels. In the absence of prior information, these data could erroneously be ascribed to the presence of protected sites. However, the observed patterns clearly originate from other factors; possibly they are caused by modulations of the amide CID efficiency by kinetic isotope effects. It is concluded that scrambling does not represent the only conceptual problem in HDX-CID studies and that control experiments on uniformly labeled samples are essential for ruling out interpretation artifacts.     

Clinical pharmacokinetic assessment of an anti-MAdCAM monoclonal antibody therapeutic by LC-MS/MS

Liquid chromatography tandem mass spectrometry (LC-MS/MS) has been shown to be a viable tool for preclinical pharmacokinetic (PK) analysis of monoclonal antibody (mAb) therapeutics. This work describes free and total PK assays for the mAb PF-00547,659 in serum of ulcerative colitis patients in a First-In-Human study [Vermeire, S. et al. Gut2011, 60 (8), 1068-1075]. The assay to measure free PF-00547,659 used immuno-enrichment with a biotinylated anti-idiotypic antibody and streptavidin magnetic beads. The total assay used enrichment by protein G magnetic beads. Following elution of PF-00547,659 from the beads, addition of an extended sequence stable isotope labeled peptide and trypsin digestion, a proteotypic peptide derived from the CDR region of the light chain of PF-00547,659 was quantified by LC-MS/MS. The free assay had a calibration range from 7.03 ng/mL to 450 ng/mL. The assay was precise and accurate with interbatch imprecision <16.5%, and interbatch inaccuracy <13.7% at all concentrations investigated during assay qualification. Results from LC-MS/MS methodologies are compared with historical immunoassay data originally acquired during the course of the clinical study. PK parameter estimates were highly correlated between the two analytical approaches. This work provides precedence that immunoaffinity LC-MS/MS can effectively be used to measure the serum concentrations of mAb therapeutics in clinical studies.     

Multiresidue analysis of multiclass pesticides in lavandin essential oil by LC/MS/MS using the scheduled selected reaction monitoring mode

In this paper we describe the development of the first multiclass pesticide residue method applied to essential oils. A total of 70 pesticides covering a wide range of polarity and currently used on essential oil crops have been included in the method. The procedure consists of a 10-fold dilution of lavandin essential oil followed by a direct injection analysis by liquid chromatography/tandem mass spectrometry. The system used is an API 4000 QTrap equipped with an electrospray ionization interface and operating in scheduled selected reaction monitoring acquisition mode. Matrix effects were evaluated by comparing the slopes of matrix-matched and solvent-based calibration curves. Weak signal suppression or enhancement (<20%) was observed for most of the compounds. Method sensitivity was determined statistically by the injection of five matrix-matched calibration curves with the distribution's normality and the variance's homogeneity checked before establishment of a suitable regression model. Limits of detection (LODs) and quantification (LOQs) were then determined using the blank standard's deviation and the slope of the mean curve. The analytical method has been validated for 67 of the 70 pesticides and meets the following LOQs: ≤1 μg/L for 9 pesticides, ≤5 μg/L for 44, ≤10 μg/L for 9, and ≤20 μg/L for 5.     

Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS

A novel MS/MS-based analysis strategy using isotopomer labels, referred to as "tandem mass tags" (TMTs), for the accurate quantification of peptides and proteins is described. The new tags are designed to ensure that identical peptides labeled with different TMTs exactly comigrate in all separations. The tags require novel methods of quantification analysis using tandem mass spectrometry. The new tags and analysis methods allow peptides from different samples to be identified by their relative abundance with greater ease and accuracy than other methods. The new TMTs permit simultaneous determination of both the identity and relative abundances of peptide pairs using a collision induced dissociation (CID)-based analysis method. Relative abundance measurements made in the MS/MS mode using the new tags are accurate and sensitive. Compared to MS-mode measurements, a very high signal-to-noise ratio is achieved with MS/MS based detection. The new tags should be applicable to a wide variety of peptide isolation methods.