Electrospray ionization tandem mass spectrometry for structural elucidation of protonated brevetoxins in red tide algae

Brevetoxins, the toxic components of "red tide" algae, all share one of two robust polycyclic ether backbone structures, but they are distinguished by differing side-chain substituents. Electrospray ionization mass spectrometry analyses of brevetoxins have shown that the polyether structure invariably has a very high affinity for sodium cations that results in the production of abundant (M + Na)+ ions even when sodium cations are only present as impurities. Because the ionic charge tends to remain localized on the sodium atom and because at least two bonds must be broken in order to produce polycyclic backbone fragmentation, it is extremely difficult to obtain abundant product ions (other than Na+) from (M + Na)+ brevetoxin precursor ions in low-energy collision-induced dissociation (CID) MS/MS experiments. This report establishes that acid additives (oxalic acid, trifluoroacetic acid, and particularly hydrochloric acid) in aqueous methanol solutions can promote high yields of protonated brevetoxin molecules (MH+ ions) for Btx-1, -2, and -9 brevetoxins. Most importantly, unlike their (M + Na)+ counterparts, MH+ precursor ions offer readily detectable product ions in CID MS/MS experiments, even under low-energy collisions. This direct structural characterization approach has provided decomposition information from brevetoxins that was previously inaccessible, including the identification of diagnostic product ions for "type A" brevetoxins (m/z 611) and "type B" brevetoxins (m/z 779, 473, 179) and characteristic ions for Btx-1 (m/z 221, 139), Btx-2 (m/z 153), and Btx-9 (m/z 157, 85). Precursor ion scans and constant neutral loss scans are proposed to enable screening of individual type A or type B brevetoxins present in naturally occurring mixtures.     

Multiplexed MS/MS in a quadrupole ion trap mass spectrometer

A multiplexing method for performing MS/MS on multiple peptide ions simultaneously in a quadrupole ion trap mass spectrometer (QITMS) has been developed. This method takes advantage of the inherent mass bias associated with ion accumulation in the QITMS to encode the intensity of precursor ions in a way that allows the corresponding product ions to be identified. The intensity encoding scheme utilizes the Gaussian distributions that characterize the relationship between ion intensities and rf trapping voltages during ion accumulation. This straightforward approach uses only two arbitrary waveforms, one for isolation and one for dissociation, to gather product ion spectra from N precursor ions in as little as two product ion spectra. In the example used to illustrate this method, 66% of the product ions from five different precursor peptide ions were correctly correlated using the multiplexing approach. Of the remaining 34% of the product ions, only 6% were misidentified, while 28% of the product ions failed to be identified because either they had too low intensity or they had the same m/z ratio as one of the precursor ions or the same m/z ratio as a product ion from a different precursor ion. This method has the potential to increase sample throughput, reduce total analysis times, and increase signal-to-noise ratios as compared to conventional MS/MS methods.     

Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides

Gas-phase fractionation (GPF) is an efficient and straightforward method to increase proteome coverage. In this report, optimal m/z ranges were calculated based on genomic complexity and experimental data. Then, theoretical precursor ion densities were calculated in silico from various organisms' genomes and found to corroborate the empirical selection of m/z ranges based on ion density mapping. According to both calculations, the choice of m/z range for most efficient GPF coverage in the lower m/z range should be very narrow and increase as m/z value increases. Next, a systematic LC-MS/MS analysis was performed to confirm this observation. The behavior of data-dependent precursor ion selection and the origin of the observed variability was investigated under three different scan modes of an LTQ-Orbitrap hybrid mass spectrometer. Finally, GPF combined with data-dependent analysis was compared to a targeted, pseudo-multiple reaction monitoring analysis of proteotypic peptides that should be, based on empirical observation of LC-ESI-MS/MS data, detectable. The result of the latter experiment supported our conclusion that data-dependent analysis using rational gas-phase fractionation was sufficient for comprehensive proteomic analysis of the proteotypic peptides in an unfractionated cell lysate.     

高效液相色谱-串联质谱法测定贻贝中腹泻性贝类毒素的含量

采用液相色谱-串联质谱法检测了贻贝中大田软海绵酸(OA)和鳍藻毒素-1(DTX-1)两种腹泻性贝类毒素的含量。样品经80%甲醇水溶液提取,Sep-pak silica固相萃取小柱净化,80%甲醇水溶液定容后供HPLC-MS/MS分析。采用电喷雾负离子模式多反应监测方式进行检测,OA和DTX-1的定量检测的离子对分别为m/z 803.5/255.1和m/z817.4/255.1。2种贝类毒素在20~800μg/L范围内线性良好;在4个添加水平下OA的回收率为79.5%～88.6%,RSD为8.43%～10.4%;DTX-1的回收率为83.8%～91.2%,RSD为4.22%～6.54%。方法灵敏度高,定量限为0.02mg/kg。来自市场和产地的45个贻贝样品残留分析发现,有4个样品检出腹泻性贝类毒素,检出率为8.9%。     

Study of the fragmentation mechanism of protonated 6-hydroxychlorzoxazone: application in simultaneous analysis of CYP2E1 activity with major human cytochrome P450s

The application of liquid chromatography tandem mass spectrometry for simultaneous analysis of major human cytochrome P450 activities via a single atmospheric pressure ionization (API) LC/MS/MS method has been hampered by the preferred detection of 6-hydroxychlorzoxazone (HCZ), the metabolite of the CYP2E1 probe, chlorzoxazone, under negative API. An initial simulation of the dissociation constants suggested the potential ionization of the enol form of HCZ at low pH, and the accurate mass measurements confirmed the presence of the protonated HCZ signal under (+) ESI at pH 3. However, the CID spectrum of the protonated HCZ resulted in a few intense, but uncommon, fragment ions that could be utilized for specific selected reaction monitoring (SRM) transitions. The deduced elemental compositions of these fragment ions indicated possible aromatic ring opening for the first two intense product ions at m/z 130 and 115, as well as chlorine radical loss for the third ion at m/z 151. Further precursor and product ion scan studies, along with the deuterium ion exchange in solution, revealed the involvement of three distinct pathways of fragmentation. The m/z 186-->130 transition, which was shown to be specific in human plasma and rat hepatic microsomes, was further combined with the SRM transition of reserpine (internal standard) and eight probe substrates for human cytochrome P450 isoforms. This led to the development of a full LC/MS/MS method capable of analyzing a total of nine human P450 activities within 3 min, including CYP2E1, using a single assay in the (+) ESI mode. The HCZ assay showed excellent linearity with a coefficient of determination (R2) greater than 0.98 at dynamic range of 0.05 (LOQ) to 40 microM. Preliminary data from the three-day validation of the HCZ assay indicated that the accuracy and precision for quality control samples was within +/- 15% of the spiked concentration at all levels.     

Investigation of the unusual behavior of metolachlor under chemical ionization in a hybrid 3D ion trap mass spectrometer

This article describes the strange behavior of the widely used herbicide metolachlor under chemical ionization conditions in a hybrid source ion trap mass spectrometer in gas chromatography/mass spectrometry (GC/MS) coupling. With the use of ammonia as the reagent gas, metolachlor provides a chlorinated ion at m/z 295/297, almost as abundant as the protonated molecule at m/z 284/286, which cannot be isolated to perform tandem mass spectrometry (MS(n)) experiments. Curiously, this ion at m/z = M + 12 is not observed for the herbicides acetochlor and alachlor, which present very similar chemical structures. The chemical structure of the m/z 295/297 ions and the explanation of the observed phenomenon based on the metastable behavior of these ions were elucidated on the basis of experiments including isotopic labeling and modifications of the operating conditions of the ion trap mass spectrometer. This work allows one to give new recommendations for an optimized use of hybrid source ion trap mass spectrometers.     

Selective detection and identification of sugar nucleotides by CE-electrospray-MS and its application to bacterial metabolomics

A novel method employing CE-ESMS and precursor ion scanning was developed for the selective detection of nucleotide-activated sugars. By using precursor ion scanning for fragment ions specific to the different nucleotide carriers, i.e., ions at m/z 322 for cytidine monophosphate, m/z 323, 385, and 403 for uridine diphosphate, m/z 362, 424, and 442, for guanosine diphosphate, and m/z 346, 408, and 426 for adenosine diphosphate, it was possible to selectively detect sugar nucleotides involved in the biosynthesis of glycoconjugates such as glycoproteins and lipopolysaccharides. Enhancement of sensitivity was achieved using N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) as a sample stacking buffer and provided detection limits between 0.2 and 3.8 pmol.mL(-)(1). The present CE-ESMS method provided linear dynamic ranges over the concentrations 0.2-164 nM (r(2) = 0.952-0.997) for different nucleotide sugar standards. The application of this method is demonstrated for the identification of intracellular pools of sugar nucleotides in wild type and isogenic mutants from the bacterial pathogen Campylobacter jejuni. By using product ion scanning (with and without front-end collision-induced dissociation), it was possible to determine the precise nature of unexpected sugar nucleotides involved in the biosynthesis of pseudaminic acid, a sialic acid-like sugar previously observed on the flagellin of some pathogenic bacteria.     

UPLC-MS/MS测定人血浆中罗红霉素的浓度及在药代动力学中的应用

建立一种快速、准确测定人血浆中罗红霉素浓度的UPLC-MS/MS分析方法。以克拉霉素为内标,0.2mL含药血浆经碱化、乙酸乙酯萃取后进样分析;色谱柱为Acquity UPLC BEH C18（2.1mm×50mm×1.7μm）,流动相组成为乙腈∶0.01%醋酸铵=30∶70,梯度洗脱方式,乙腈比例在4 min内从30%变为70%,流速0.3 mL/min,柱温为35℃,进样量3μL。质谱条件：气动辅助电喷雾离子化（ESI）源;正离子检测（MRM）模式,罗红霉素质荷比为（m/z 837.53→m/z 158.15）和克拉霉素质荷比为（m/z 748.48→m/z 590.30）。罗红霉素在0.05~25.6μg/mL的浓度范围内呈线性,定量下限为0.05μg/mL,基质效应影响小,日内变异系数小于10.3%,日间变异系数小于9.4%,相对回收率在97.5%~106.4%之间。该方法准确、快速、灵敏,可用于微量血浆的罗红霉素药物浓度监测、人体内药代动力学及生物等效性研究。     

Simultaneous characterization of perfluoroalkyl carboxylate, sulfonate, and sulfonamide isomers by liquid chromatography-tandem mass spectrometry

A comprehensive method was developed to simultaneously separate and detect perfluorinated acid (PFA) and PFA-precursor isomers using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A linear perfluorooctyl stationary phase and acidified mobile phase increased separation efficiency, relative to alkyl stationary phases, for the many perfluoroalkyl carboxylate (PFCA), perfluoroalkyl sulfonate (PFSA), and perfluorooctyl sulfonamide (PFOSA) isomers and in combination with their distinct MS/MS transitions allowed full resolution of most isomers in standards. Utilizing the absence of the "9-series" and "0-series" product ions, several perfluorooctane sulfonate (C8F17SO3-, PFOS) isomers were structurally elucidated. In human serum, only perfluorooctane sulfonamide (C8F17SO2NH2, FOSA) and PFOS consisted of significant quantities of branched isomers, whereas PFCAs were predominantly linear. Interferences that coelute with the m/z 499 --> 80 transition of PFOS on alkyl stationary phases were simultaneously separated and identified as taurodeoxycholate isomers, removal of which permitted the use of the more sensitive m/z 80 product ion and a resulting 20-fold decrease in PFOS detection limits compared to the m/z 499 --> 99 transition (0.8 pg versus 20 pg using m/z 80 and 99, respectively). Interferences in human serum which caused a 10-20-fold over-reporting of perfluorohexane sulfonate (C6F13SO3-, PFHxS) concentrations on alkyl stationary phases were also simultaneously separated from linear PFHxS and identified as endogenous steroid sulfates. PFOSA isomers, generated with human microsomes, had different rates of metabolism, suggesting that the perfluoroalkyl branching pattern may affect the biological properties of individual isomers. This fact, and for reasons of improved accuracy and sensitivity, investigators are urged to utilize more efficient separation methods capable of isomer characterization in perfluoroalkyl research.     

High-throughput screening and characterization of reactive metabolites using polarity switching of hybrid triple quadrupole linear ion trap mass spectrometry

A highly sensitive and efficient method has been developed for detection and characterization of glutathione (gamma-glutamyl-cysteinylglycine, GSH)-trapped reactive metabolites using a negative precursor ion (PI) as the survey scan to trigger the acquisition of positive enhanced product ion (EPI) spectra on a triple quadrupole linear ion trap mass spectrometer. The negative precursor ion scan step was carried out monitoring the anion at m/z 272, corresponding to deprotonated gamma-glutamyl-dehydroalanyl-glycine originating from the glutathionyl moiety. Because of the uniqueness and abundance of the anion at m/z 272, this single survey scan exhibited broad utility in the detection of unknown GSH conjugates. Further structural characterization was achieved by analyzing positive MS2 spectra that featured rich fragments without mass cutoff and were acquired in the same liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. The effectiveness and reliability of this approach was evaluated using a number of model compounds in human liver microsomal incubations, including acetaminophen, clozapine, diclofenac, imipramine, meclofenamic acid, and ticlopidine. As a result, the PI-EPI approach revealed the presence of known adducts and, in many instances, identified additional conjugates that had not been reported previously. In comparison to the widely used neutral loss (NL) scanning analysis, this approach provided superior sensitivity and selectivity for different types of GSH conjugates. More importantly, the PI-EPI approach is suitable for high-throughput screening of reactive metabolites in the drug discovery process.     

Development and evaluation of a candidate reference method for the determination of total cortisol in human serum using isotope dilution liquid chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry

Cortisol is an important diagnostic marker for the production of steroid hormones, and accurate measurements of serum cortisol are necessary for proper diagnosis of adrenal function. A candidate reference method involving isotope dilution coupled with liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) has been developed and critically evaluated. An isotopically labeled internal standard, cortisol-d(3), was added to serum, followed by equilibration and solid-phase and ethyl acetate extractions to prepare samples for liquid chromatography/mass spectrometry electrospray ionization (LC/MS-ESI) and liquid chromatography/tandem mass spectrometry electrospray ionization (LC/MS/MS-ESI) analyses. (M + H)(+) ions at m/z 363 and 366 for cortisol and its labeled internal standard were monitored for LC/MS. The transitions of (M + H)(+) --> [(M + H)(+) - 2H(2)O] at m/z 363 --> 327 and 366 --> 330 were monitored for LC/MS/MS. The accuracy of the measurement was evaluated by a comparison of results of this candidate reference method on lyophilized human serum reference materials for cortisol [Certified Reference Materials 192 and 193] with the certified values determined by gas chromatography/mass spectrometry reference methods and by a recovery study for the added cortisol. The results of this method for total cortisol agreed with the certified values within 1.1%. The recovery of the added cortisol ranged from 99.8% to 101.0%. This method was applied to the determination of cortisol in samples of frozen serum pools. Excellent precision was obtained with within-set CVs of 0.3%-1.5% and between-set CVs of 0.04%-0.4% for both LC/MS and LC/MS/MS analyses. The correlation coefficients of all linear regression lines ranged from 0.998 to 1.000. The detection limits (at a signal-to-noise ratio of approximately 3-5) were 10 and 15 pg for LC/MS and LC/MS/MS, respectively. This method, which demonstrates good accuracy and precision, and is free from interferences from structural analogues, qualifies as a candidate reference method and can be used as an alternative reference method to provide an accuracy base to which the routine methods can be compared.     

Derivatization of ethinylestradiol with dansyl chloride to enhance electrospray ionization: application in trace analysis of ethinylestradiol in rhesus monkey plasma

The extensive metabolism and administration of low doses of ethinylestradiol (EE) in preclinical animal species necessitates a sensitive analytical method to quantify the drug at low picogram-per-milliliter concentrations in biological matrixes. A highly sensitive and accurate method based on the derivatization of EE with dansyl chloride coupled with liquid chromatography/tandem mass spectrometry is described. The dansyl derivatization of EE introduced a basic secondary nitrogen into the molecule that was readily ionized in commonly used acidic HPLC mobile phases. The derivative showed an intense protonated molecular ion at m/z 530 under positive turbo ion spray ionization. The collision-induced dissociation of this ion formed a distinctive product at m/z 171, corresponding to the protonated 5-(dimethylamino)naphthalene moiety. The selected reaction monitoring, based on the m/z 530 --> 171 transition, was highly specific for EE, since no background signal was observed from blank plasma obtained from rhesus monkeys. The limit of detection, at a signal-to-noise ratio of 5, was 0.2 fg/mL EE spiked into blank plasma. This allowed for a lower limit of quantitation of 5 pg/mL using a 50-microL plasma sample and 10-microL injection of dansylated derivative into the CTC-PAL Leap autosampler coupled to a Sciex API 4000 mass spectrometer. Using fast-gradient liquid chromatography, the analyte peak eluted at 1.6 min. The validation results showed high accuracy (% bias < 4) and precision (% CV < 7.5) at broad linear dynamic ranges (0.005-20 ng/mL), using deuterated EE as internal standard. Therefore, the facile dansyl derivatization coupled with tandem mass spectral analysis allowed the development of a highly sensitive and specific method for quantitation of trace levels of EE in the plasma of rhesus monkeys dosed orally and intravenously with EE.     

Parent and neutral loss monitoring on a quadrupole ion trap mass spectrometer: screening of acylcarnitines in complex mixtures

A novel and practical technique for performing both parent and neutral loss (P&NL) monitoring experiments on a quadrupole ion trap mass spectrometer is presented. This technique is capable of performing scans analogous to the parent and neutral loss scans routinely applied on tandem-in-space instruments and allows for the screening of a sample to detect analytes of a specific compound class on a chromatographic time-scale. Acylcarnitines were chosen as the model compound class to demonstrate the analytical utility of P&NL monitoring because of their amenability to electrospray ionization (ESI), their unique and informative MS/MS fragmentation pattern, and their importance in biological functions. The [M + H]+ ions of all acylcarnitines dissociate to produce neutral losses of 59 and 161 amu and common product ions at m/z 60, 85, and 144. Both the neutral loss monitoring of 59 amu and the parent ion monitoring of m/z 85 are shown to be capable of identifying acylcarnitine [M + H]+ ions in a synthetic mixture and spiked pig plasma. The neutral loss monitoring of 59 amu is successful in detecting acylcarnitines in an unspiked pig plasma sample.     

Fast atom bombardment tandem mass spectrometric identification of diacyl, alkylacyl, and alk-1-enylacyl molecular species of glycerophosphoethanolamine in human polymorphonuclear leukocytes.

Fast atom bombardment ionization with tandem mass spectrometry of both positive and negative ions is a useful technique for the identification of intact glycerophosphoethanolamine (GPE) phospholipids, providing information as to polar head group and fatty acyl substituents. In the identification of GPE molecular species, positive ion neutral loss scanning for 141 units was attempted to confirm the presence of the phosphoethanolamine polar head group. This scan was found to discriminate against the abundant subclass of phospholipids having an 1-O-alk-1'-enyl linkage, termed plasmalogens, as well as 1-O-alkyl ether species. The neutral loss process is suggested to involve attack of a carbonyl oxygen from either sn-1 or sn-2 on the sn-3 methylene carbon with loss of neutral phosphoethanolamine. Using FAB/MS/MS alone, it is not possible to differentiate between plasmalogens and other 1-O-alkyl ether molecular species having the same molecular weight. The combination of mild acid hydrolysis, which selectively hydrolyzes the labile 1-O-alk-1'-enyl bond, with subsequent FAB/MS/MS distinguished species of these distinct subclasses. Using these techniques and precursor ion scans for the arachidonoyl carboxylate anion, m/z 303, the arachidonic acid containing glycerophosphoethanolamine molecular species were identified and the relative abundance of arachidonoyl plasmalogen, alkylacyl, and 1,2-diacyl GPE molecular species in the human polymorphonuclear leukocyte (neutrophil) was determined to be 75.4%, 12.1%, and 12.5%, respectively. These values were not significantly different from that reported in the literature using conventional methodology.     

Matrix-assisted laser desorption/ionization-ion mobility separation-mass spectrometry imaging of vinblastine in whole body tissue sections

During early-stage drug development, drug and metabolite distribution studies are carried out in animal tissues using a range of techniques, particularly whole body autoradiography (WBA). While widely employed, WBA has a number of limitations, including the following: expensive synthesis of radiolabeled drugs and analyte specificity and identification. WBA only images the radiolabel. MALDI MSI has been shown previously to be advantageous for imaging the distribution of a range of drugs and metabolites in whole body sections. Ion mobility separation (IMS) adds a further separation step to imaging experiments; demonstrated here is MALDI-IMS-MS whole body imaging of rats dosed at 6 mg/kg i.v. with an anticancer drug, vinblastine and shown is the distribution of the precursor ion m/z 811.4 and several product ions including m/z 793, 751, 733, 719, 691, 649, 524, and 355. The distribution of vinblastine within the ventricles of the brain is also depicted. Clearly demonstrated in these data are the removal of interfering isobaric ions within the images of m/z 811.4 and also of the transition m/z 811-751, resulting in a higher confidence in the imaging data. Within this work, IMS has shown to be advantageous in both MS and MS/MS imaging experiments by separating vinblastine from an endogenous isobaric lipid.     

Simultaneous analysis of amino acids and carboxylic acids by capillary electrophoresis-mass spectrometry using an acidic electrolyte and uncoated fused-silica capillary

A simple, low-cost capillary electrophoresis-mass spectrometry (CE-MS) method is demonstrated for the simultaneous analysis of amino acids and small carboxylic acids (glycerate, lactate, fumarate, succinate, malate, tartrate, citrate, iso-citrate, cis-aconitate, and shikimate). All CE-MS experiments were performed using a single uncoated fused-silica capillary and with a single separation electrolyte, formic acid. For CE polarity, the CE inlet was set as the anode, and the MS side was set as the cathode. By using high-speed sheath gas flow, the apparent mobilities of all compounds were sped up; thus, the migration times of the carboxylic acids were reduced. In positive ion mode ESI-MS detection, small carboxylic acids were detected faintly as m/z = [M + 18](+) or [M + 23](+), after protonated molecule detection (m/z = [M + 1](+)) of the amino acids. In negative ion mode, all of these small carboxylic acids were detected clearly as deprotonated molecules (m/z = [M - 1](-)), after detection of the amino acids. By changing the polarity of the MS during CE separation, both amino acids and small carboxylic acids were detectable in a single electrophoresis analysis run. With this method, the diurnal metabolic changes of pineapple leaves were observed as reflecting Crassulacean acid metabolism.     

Exploring the precursor ion exclusion feature of liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry for improving protein identification in shotgun proteome analysis

In shotgun proteome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS), not all coeluting peptides at a given retention time are subjected to MS/MS due to the limitation of spectral acquisition speed of a mass spectrometer. In this work, precursor ion exclusion (PIE) in an electrospray ionization (ESI) quadrupole time-of-flight (QTOF) mass spectrometer was explored as a means of mitigating the undersampling problem. This strategy is based on running replicates of the sample where the precursor ions detected in the initial run(s) are excluded for MS/MS in the subsequent run. Four PIE methods as well as running replicates without PIE were investigated and compared for their effectiveness in identifying peptides and proteins. In the analysis of an MCF-7 breast cancer cell lysate digest by three replicate 2 h gradient LC-ESI runs, the first PIE method used a list of precursor ions detected in the initial run(s) for exclusion and identified a total of 572 proteins from the three runs combined with an average of 3.59 peptides matched to a protein. The second PIE method involved in the generation of a list of m/ z values of precursor ions along with their retention time information from the initial run(s), followed by entering these ions with retention times into the ion exclusion program of the QTOF control software for exclusion at a predefined retention time window (i.e., +/-150 s). In comparison to the first PIE method, this method reduced the possibility of excluding different peptide ions of the same m/ z (within a mass tolerance window) eluted at different retention windows. A total of 657 proteins were identified with an average of 3.75 peptides matched to a protein. The third PIE method studied relied on the exclusion of the precursor ions of peptides identified through database search of the MS/MS spectra generated in the initial run(s). This selective PIE method identified a total of 681 proteins with an average of 3.68 peptides matched to a protein. The final PIE method investigated involves the expansion of the selective PIE list by including nonidentifiable peptide ions found in the database search. This complete PIE method identified a total of 726 proteins with an average of 3.66 peptides per protein. In the case of three replicate runs without PIE, a total of 460 proteins were identified with an average of 3.51 peptides matched to a protein. Thus, the use of an optimal PIE strategy significantly increased the number of proteins identified from replicate runs (i.e., 726 vs 460 or a 58% increase). It is further demonstrated that this PIE strategy also improves protein identification efficiency in the analysis of a yeast whole cell lysate digesta less complex proteome digest. A total of 533 proteins identified from five replicate runs with complete PIE, compared to 353 proteins identified from the five replicate runs without PIE, representing a 51% increase in the number of proteins identified.     

Scrubbing ions with molecules: kinetic studies of chemical noise reduction in mass spectrometry using ion-molecule reactions with dimethyl disulfide

The kinetics and product distributions of the reactions of dimethyl disulfide (DMDS) have been investigated with a group of chemical background ions commonly observed in atmospheric pressure ionization (API) mass spectrometry (MS) in order to assess the value of this molecule in filtering (or "scrubbing") these ions by changing their mass/charge (m/z) ratio. The measurements were taken with a novel electrospray ionization/selected ion flow tube/QqQ tandem mass spectrometer. The background ions studied include those with m/z 42 (protonated acetonitrile, ACN), 83 (protonated ACN dimer), 99 (protonated phosphoric acid), 117 (water cluster of m/z 99), 131 (methanol cluster of m/z 99), 149 (protonated phthalic anhydride, formed from the phthalates), and 327 (protonated triphenyl phosphate). In addition, reactions of DMDS have been studied with two model analytes--protonated caffeine and doubly protonated bradykinin--in order to assess the selectivity of DMDS reactivity. All the measurements were taken at 295 +/- 2 K in helium buffer gas at a pressure of 0.35 +/- 0.01 Torr. DMDS was observed to react efficiently with m/z 42 (ACNH+), 149 (from phthalates), and 99 (protonated phosphoric acid), with k/kc=0.91, 0.47, and 0.38, respectively. Only proton transfer was observed with ACNH+, followed by the secondary reaction of [DMDSH]+ with DMDS to yield [CH3S-S(CH3)-SCH3]+. Ligation of DMDS was the dominant primary channel observed for the reaction of the m/z 149 background ion; however, some proton transfer also was observed. Both of these primary product ions react further with DMDS to yield [CH3S-S(CH3)-SCH3]+, the structure of which we have determined computationally using DFT calculations. Only the sequential ligation with two DMDS molecules was observed for the reaction of the m/z 99 ion. Reactions of DMDS with m/z 117 [H3PO4 + H + H2O]+ and m/z 131 [H3PO4 + H + MeOH]+ were observed to proceed with k/kc=0.71 and 0.058, respectively. Ligand substitution of DMDS for H2O predominated ( approximately 94%) over DMDS ligation ( approximately 6%) in the reaction with m/z 117, while only DMDS ligation was observed for the reaction of m/z 131 with DMDS. In contrast, the reactions of DMDS with ions of m/z 83 (protonated dimer of ACN) and 327 (protonated triphenyl phosphate) were extremely inefficient, with k/kc=0.0042 and 0.0079, respectively. The higher reactivity of DMDS toward ACNH+ (m/z 42) compared to (ACN)2H+ (m/z 83) is attributed to the lower proton affinity of the unsolvated ACN. The reactivity of DMDS toward the two model analyte ions studied-protonated caffeine and doubly protonated bradykinin-was negligible, with k/kc=0.0073 and 0.010, for the respective reactions. These results suggest that, under appropriate reagent pressure conditions, DMDS can be an appropriate reagent for chemically filtering out many common API-MS background ions, without significantly affecting the observed intensity of analyte peaks.     

Determination of linear alkylbenzenesulfonates and their degradation products in soils by liquid chromatography-electrospray-ion trap multiple-stage mass spectrometry

Linear alkylbenzenesulfonates (LAS) (C(10)-C(13)) and their degradation products, sulfophenyl carboxylate compounds (SPCs) (C(2)-C(6), C(8), C(11)), have been extracted from soil samples with methanol, isolated, concentrated by solid-phase extraction, and determined by liquid chromatography/negative ion electrospray quadrupole ion-trap tandem mass spectrometry (MS(n)). The ion fragmentation processes and pathways were studied in detail by MS, MS(2), and MS(3). Upon collision-induced dissociation, the deprotonated molecules of LASs render the ethylene-substituted benzenesulfonate ion (m/z 183), the fragmentation of which gave the intense signal at m/z 119, corresponding to the ethylene-substituted phenoxide ion formed by the loss of sulfur dioxide. The fragmentation pattern of SPCs shows that, for the analytes of large carbon atom chains (>5C), the neutral loss of water is favored whereas for those of short carbon atoms chain, the loss of carbon dioxide is more frequent. Multiple reaction monitoring using isolation only for MS and using isolation and fragmentation for MS(2) and MS(3) were used to identify and quantify each compound. The three MS modes have been validated in terms of sensitivity, selectivity, and precision, showing that each MS stage used reduces sensitivity 10 times. Recoveries from soil were higher than 65% at LOQ level for all the analytes tested, except for C(2)-C(4) SPCs by any MS mode, with relative standard deviation lower than 19%. The utility of the method is demonstrated by successfully quantifying real samples treated with these products. Quantification limits for the methodology developed in this work ranged from 0.5 to 50 microg kg(-1) by MS, from 2 to 400 microg kg(-1) by MS(2), and from 20 to 4000 microg kg(-1) by MS(3). Concentration levels of LASs and SPCs-ranging from 0.1 to 15 mg kg(-1)-were found in soil samples amended with sludges, thus indicating their input and persistence in the soil compartment.