Low-energy Collision-induced Dissociation Tandem Mass Research Articles

FPTMS: Frequency-based approach to identify the peptide from the low-energy collision-induced dissociation tandem mass spectra

The database search method is a widely accepted method to assign a peptide to the tandem mass spectra. In this study, a new flexible method- FPTMS is introduced to interpret the tandem mass spectra with the known peptide sequences in a protein database. Here the frequency of occurrence of fragment ion peaks extracted from the extensive spectral library is used to predict the theoretical tandem mass spectra of the peptides. The dot product scoring and windowed-xcorr scoring methods were implemented to score the experimental spectrum against the theoretical peptide spectra. Windowed-xcorr is introduced to tackle the mass errors and the cleavage position of the fragmentation process. The new method with windowed-xcorr shows an improved identification rate compared to the existing search engines Crux-Tide and X!Tandem at 1% False Discovery Rate (FDR) for the dataset considered in this study. SignificanceIdentifying or sequencing of the peptide from tandem mass spectra is an important application in mass spectrometry-based proteomics. Collision-induced dissociation (CID) fragmentation spectra have been widely used to develop a peptide identification algorithm using database search strategy. CID fragmentation behavior is a complex process and found to have dependency on the sequences of peptide, charge state, and residue content. The inclusion of more features of peptide fragmentation behavior and adaptable scoring algorithm improves the efficiency of the peptide identification algorithm.

Top-down lignomics analysis of the French pine lignin by atmospheric pressure photoionization quadrupole time-of-flight tandem mass spectrometry: Identification of a novel series of lignin-carbohydrate complexes.

We report the top-down lignomics analysis of the virgin released lignin (VRL) extracted from French pine wood by using atmospheric pressure photoionization quadrupole time-of-flight mass spectrometry (APPI-QqTOF-MS) and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS). We used APPI-QqTOF-MS (positive ion mode) for the analysis of the complex mixture of VRL oligomers extracted from French pine wood. Some of the major precursor ions were fished out from the complex VRL oligomeric mixture and subjected to low-energy CID-MS/MS analyses. Fourteen novel lignin-carbohydrate complexes (LCCs) were identified using APPI-QqTOF-MS/MS of the very complex mixture of virgin released lignins (VRLs), directly extracted from French pine wood without any kind of purification. The low-energy CID-MS/MS analyses allowed us to establish the fragmentation patterns of the precursor ions and to identify the complex structures of the identified LCC molecules. These novel identified series of LCCs were composed of one or two carbohydrate rings to which one, two, or three lignin units were covalently attached. In addition to the fourteen LCCs, acetyl eugenol was identified in the French pine VRL sample. The identification of acetyl eugenol indicates possible lignin degradation and modification (acetylation) during the mild extraction method developed by the Compagnie Industrielle de la Matière Végétale (CIMV). The top-down lignomics analysis of the French pine VRLs using APPI-QqTOF-MS and low energy CID-MS/MS allowed us to identify acetylated eugenol and a novel series of fourteen LCCs. These series of LCCs provide evidence that lignins are covalently linked to carbohydrates in the native wood network and act as cross-linkers between cellulose and hemicellulose components of wood.

Electron ionization mass spectrometric fragmentation and detection of autoxidation products of 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene in Arctic sediments.

Some highly branched isoprenoid (HBI) alkenes are commonly used as proxies for palaeoceanographic reconstructions. However, there is a need to identify compounds that are sufficiently stable and abundant to be used as tracers of HBI oxidation in sediments. 2,6,10,14-Tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5(Z/E)-en-4-ols resulting from 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene appear to be useful for this purpose. Comparison of electron ionization (EI) mass spectra and retention times with those of standards allowed formal identification of autoxidation products of 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene. EI-MS fragmentations of TMS ethers of the main oxidation products (2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5(Z/E)-en-4-ols) were deduced by gas chromatography/electron ionization mass spectrometry (GC/EI-MS), low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) and accurate mass measurements. These compounds were then quantified in Arctic sediment samples in MS/MS multiple reaction monitoring (MRM) mode using transitions based on the main fragmentation pathways elucidated. 2,6,10,14-Tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5(Z/E)-en-4-ols were identified after autoxidation of the HBI alkene 2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-ene. Low-energy CID-MS/MS analyses and accurate mass measurements allowed the EI-MS fragmentation pathways of their trimethylsilyl (TMS) derivatives to be elucidated. Some specific fragment ions and chromatographic retention times were also useful for further characterization. As an application of some of the described fragmentations, TMS derivatives of these metabolites were characterized and quantified in MRM mode in Arctic sediments. Due to their production in high proportions during autoxidation of their parent HBI diene, their apparent stability in sediments, and their specific EIMS fragmentations, (Z and E)-2,6,10,14-tetramethyl-7-(3-methylpent-4-enyl)-pentadec-5-en-4-ol TMS derivatives appeared to be useful tracers of HBI autoxidation in sediments.

Structural investigation by tandem mass spectrometry analysis of a heterogeneous mixture of Lipid An isolated from the lipopolysaccharide of Aeromonas hydrophila SJ-55Ra.

We report herein the electrospray ionization mass spectrometry (ESI-MS) negative ion mode and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) analysis of a mixture of lipid An isolated from the lipopolysaccharide (LPS) of a rough-resistant wild strain of the Gram-negative bacteria Aeromonas hydrophila grown in the presence of phages (SJ-55Ra). This investigation indicates that the presence of a mixture of lipid A acylated disaccharides, whose molecular structures were not relatively conserved, resulted from the incomplete LPS biosynthesis caused by the phage treatment. The heterogeneous lipid An mixture from the LPS-SJ55Ra was obtained following growth of the Gram-negative bacteria Aeromonas hydrophila (SJ-55R) in the presence of phages and isolation by the aqueous phenol method. Following hydrolysis and purification of the lipopolysaccharide, ESI-MS and low-energy CID-MS/MS analyses were performed on a triple-quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) instrument. ESI-MS analysis suggested that this lipid An mixture contained eight molecular disaccharide anions and three monosaccharide anions. This series of lipid An was asymmetrically substituted with ((R)-14:0(3-OH)) fatty acids located at O-3 and N-2 and with branched fatty acids: (Cl4:0(3-(R)-O-C14:0)) and (C12:0(3-(R)-O-(14:0)) at the O-3' and N-2' positions. Tandem mass spectrometric analyses allowed the exact determination of the fatty acid acylation locations on the D-GlcpN disaccharide. The MS/MS results established that it was possible to selectively cleave C-O, C-N, and C-C bonds, together with glycosidic C-O and cross-ring cleavages, affording excellent structural analysis of lipid A biomolecules.

The application of multiple analyte adduct formation in the LC-MS3 analysis of valproic acid in human serum.

LC-MS using electrospray ionisation (negative ion mode) and low-energy collision-induced dissociation tandem mass spectrometric (CID-MS/MS) analysis, together with the multiple analyte adduct formation with the components of the mobile phase, were applied to analyse valproic acid in human serum with LC-MS3. The CID-fragmentation of the precursor analyte adduct [M+2CH3COONa-H]- was applied in the method validation (307.1/225.1/143.0). Chromatographic separation was performed with a Luna 5μm C18 (2) 100A, 150mm×2mm column and the elution with a mobile phase consisting of A (H2O/methanol=95/5, v/v) and B (H2O/methanol=3/97, v/v), both with 10mM ammonium acetate and 0.1% acetic acid. A binary flow pumping mode with a total flow rate of 0.400mL/min was used. The calculated limit of detection/quantification of the method calibrated in the range of 10-200μg/mL was 0.31/1.0μg/mL. The sample preparation based on protein precipitation with 1mL of H2O/methanol solution (3/97, v/v) with 10mM sodium acetate and 100mM acetic acid. On the basis of the experiments performed could be demonstrated, that multiple analyte adduct formation can be applied to generate MS3 quantitation of analytes with problematic fragmentation. The presented new strategy makes the analysis of small drugs, which do not produce any stable product ions at all, on the basis of LC-MS3 possible.

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873–875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194–10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis.

Tandem mass spectrometry determination of the putative structure of a heterogeneous mixture of Lipid As isolated from the lipopolysaccharide of the Gram-negative bacteria Aeromonas liquefaciens SJ-19a.

We report herein the electrospray ionization mass spectrometry (ESI-MS) and low-energy collision-induced dissociation tandem mass spectrometry analysis (CID-MS/MS) of a mixture of lipid As isolated from the rough lipopolysaccharide (LPS) of the mutant wild strain of the Gram-negative bacteria Aeromonas liquefaciens (SJ-19a, resistant) grown in the presence of phages. The interaction between the phages and the Gram-negative bacteria regulates host specificity and the heterogeneity of the lipid A component of the LPS. The heterogeneous mixture of lipid As was isolated by the aqueous phenol method from the LPS of the rough wild strain of Gram-negative bacteria Aeromonas liquefaciens (SJ-19a). Hydrolysis of the LPS was with 1% acetic acid, and purification was by chromatography using Sephadex G-50 and Sephadex G-15. ESI-MS and low-energy CID-MS/MS analyses were performed with a triple-quadrupole (QqQ) and a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Preliminary analysis of the lipid As mixture was conducted by ESI-MS in the negative ion mode and the spectrum obtained suggested that the lipid A SJ-19a was composed of a heterogeneous mixture of different lipid A molecules. CID-MS/MS experiments confirmed the identities of the various mono-phosphorylated β-D-GlcpN-(1→6)-α-D-GlcpN disaccharide entities. This lipid As mixture was asymmetrically substituted with fatty acids such as ((R)-14:0(3-OH)), (14:0(3-(R)-(O-12:0)) and (14:0(3-(R)-O-(14:0)) located on the O-3, O-3', N-2 and N-2' positions, respectively. Low-energy collision-induced dissociation tandem mass spectrometry in-space (QqQ-MS/MS) and in-time (FTICR-MS/MS) allowed the exact determination of the fatty acid acylation positions on the H2 PO3 →4-O'-β-D-GlcpN-(1→6)-α-D-GlcpN disaccharide backbones of this heterogeneous mixture of lipid As , composed inter alia of seven different substituted lipid As , formed from the incomplete biosynthesis of their respective LPS.

Gas-phase structures and proton affinities of N-terminal proline containing b2+ ions from protonated model peptides

In this study, we investigated the effect of the second amino acid identity of hexapeptides on gas-phase structures and the proton affinities of N-terminal proline containing b2+ ions produced from the fragmentation of b6+ ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b2+ and nominally b4+ (AAAA) ions ([M+H]+→b6+→b2+ (PX+)+b4+ (AAAA+) were mainly considered in this study. This is a unique example of consecutive cleavage of b6+ ions which fragments to b2+ and nominal b4+ ions. All structural and proton affinity calculations for b2+ ions were carried out with the B3LYP/6-31+G(d,p) level of theory. The study utilized C-terminal amidated model peptides consisting of PAAAAA-NH2 and PXAAAA-NH2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b2+ ions, namely oxazolone and diketopiperazine, have been considered for the computations. The results demonstrated that the proton affinities of oxazolone isomers of PX are greater than its diketopiperazine isomers. Higher correlation coefficient is calculated if the structure of PX is considered as oxazolone rather than diketopiperazine isomer. Additionally, a linear fit is observed between intensity ratio (PX/AAAA) and calculated proton affinities of PX ions. Additionally, MS/MS results revealed that the relative intensities of b2+-PA, PF, and PE- ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b2+-PW and PH- ions have higher relative intensities compared to the AAAA ion. This behavior is explained by the proton affinities of fragment ions computationally.

Gas-phase fragmentation of the N-oxide and N-hydroxylated derivatives of retrorsine using liquid chromatography/electrospray ionization quadrupole time-of-flight tandem mass spectrometry.

We report the electrospray ionization mass spectrometry and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) analysis of a pyrrolizidine alkaloid extract containing both retrorsine [C18H25NO6] and its N-oxide [C18H25NO7] and N-hydroxyl [C18H26NO7] derivatives measured with a QqTOFMS hybrid instrument. A solution of the pyrrolizidine alkaloid extract containing retrorsine and its N-oxide and N-hydroxyl derivatives was directly infused into an electrospray ionization-quadrupole-time-of-flight (ESI-QTOF) mass spectrometer and product ion scans of the protonated molecules of each species were acquired. Labile protons of each compound were deuterated and computational energy calculations of the proposed structures of the product ions were used to determine the fragmentation pathways of retrorsine and its N-oxide and N-hydroxyl derivatives. ESI-MS of the pyrrolizidine alkaloid extract containing retrorsine and its N-oxide and N-hydroxyl derivatives afforded the protonated retrorsine [M1 + H](+) at m/z 352.1760 and the protonated retrorsine N-oxide [M2 + H](+) at m/z 368.1631 in addition to the formation of the unexpected protonated N-hydroxyl radical [M3 + H](+•) at m/z 369.1686. CID-MS/MS of this series of protonated molecules allowed the evaluation of their gas-phase fragmentations and the establishment of their fragmentation pathways. It was also found that several product ions could be assigned to different structures. Deuterium exchange and computational energy calculations allowed us to determine the most probable structures for the characterized product ions. To our knowledge, the identification of the protonated retrorsine N-hydroxyl radical [M3 + H](+•) is reported for the first time. In addition, the MS/MS results can be used for the identification of retrorsine and its N-oxide and N-hydroxyl derivatives in different complex biological matrices.

The in situ gas-phase formation of a C-glycoside ion obtained during electrospray ionization tandem mass spectrometry. A unique intramolecular mechanism involving an ion-molecule reaction.

This study examines the electrospray ionization mass spectrometry (ESI-MS), in-source collision-induced dissociation (CID) fragmentation and low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) of a synthetic pair of β- and α-anomers of the amphiphilic cholesteryl polyethoxy neoglycolipids containing the 2-azido-2-deoxy-D-galactosyl-D-GalN3 moiety. We describe the novel and unique in situ gas-phase formation of a C-glycoside ion formed during all these gas-phase processes and propose a reasonable mechanism for its formation. The synthetic amphiphilic glycolipids were composed of the 2-deoxy-2-azido-D-galactosyl moiety (GalN3, the hydrophilic part) covalently attached to a polyethoxy spacer which is covalently linked to the cholesteryl moiety (hydrophobic part). The 2-azido-2-deoxy-α- and β-D-galactosyl-containing glycolipids were studied by in-time and in-space ESI-MS and CID-MS/MS in positive ion mode, with quadrupole ion trap (QIT), quadrupole-quadrupole-time-of-flight (QqTOF), and Fourier transform ion cyclotron resonance (FTICR) instruments. Conventional single-stage ESI-MS analysis showed the formation of the protonated molecule. During the single-stage ESI-MS analysis and the CID-MS/MS of the [M+H](+) and [M+NH4](+) adducts obtained from both glycolipid anomers, the presence of a series of specific product ions with different intensities was observed, consistent with the [C-glycoside+H-N2](+), [cholestadiene+H](+), 2-deoxy-2-D-azido-galactosyl [GalN3](+), [GalNH](+) and [sugar-Spacer+H](+) ions. The gas-phase formation of the [C-glycoside+H-N2](+) ion isolated from the glycolipid anomers was observed during both the ESI-MS of the glycolipids and the CID-MS/MS analyses of the [M+H](+) ions and it was found to occur by an intramolecular rearrangement involving an ion-molecule complex. CID-QqTOF-MS/MS and CID-FTICR-MS(2) analysis allowed the differentiation of the two glycolipid anomers and showed noticeable variation in the intensities of the product ions.

Characterizing changes in snow crab (Chionoecetes opilio) cryptocyanin protein during molting using matrix‐assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry

We report the matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) characterization of the cryptocyanin proteins of the juvenile Chionoecetes opilio crabs during their molting and non-molting phases. In order to assess the structural cryptocyanin protein differences between the molting and non-molting phases, the obtained peptides were sequenced by MALDI low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS). The cryptocyanin protein was isolated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by MALDI-TOF/TOF-MS. The purified cryptocyanin protein was sequenced, using the 'bottom-up' approach. After tryptic digestion, the peptide mixture was analyzed by MALDI-QqTOF-MS/MS and the data obtained were used for the peptide mass fingerprinting (PMF) identification by means of the Mascot database. It was demonstrated using MALDI-TOF/TOF-MS that the actual molecular weights of the non-molting and molting cryptocyanin proteins were different; these were, respectively, 67.6 kDa and 68.1 kDa. Using low-energy CID-MS/MS we have sequenced the trytic peptides to monitor the differences and similarities between the cryptocyanin molecular structures during the molting and non-molting stages. We have demonstrated for the first time that the actual molecular masses of the cryptocyanin protein during the molting and non-molting phases were different. The MALDI-CID-MS/MS analyses allowed the sequencing of the cryptocyanins after tryptic digestion, during the molting and non-molting stages, and showed some similarities and staggering differences between the identified cryptocyanin peptides.

An online nano‐LC‐ESI‐FTICR‐MS method for comprehensive characterization of endogenous fragments from amyloid β and amyloid precursor protein in human and cat cerebrospinal fluid

Amyloid precursor protein (APP) is the precursor protein to amyloid β (Aβ), the main constituent of senile plaques in Alzheimer's disease (AD). Endogenous Aβ peptides reflect the APP processing, and greater knowledge of different APP degradation pathways is important to understand the mechanism underlying AD pathology. When one analyzes longer Aβ peptides by low-energy collision-induced dissociation tandem mass spectrometry (MS/MS), mainly long b-fragments are observed, limiting the possibility to determine variations such as amino acid variants or post-translational modifications (PTMs) within the N-terminal half of the peptide. However, by using electron capture dissociation (ECD), we obtained a more comprehensive sequence coverage for several APP/Aβ peptide species, thus enabling a deeper characterization of possible variants and PTMs. Abnormal APP/Aβ processing has also been described in the lysosomal storage disease Niemann-Pick type C and the major large animal used for studying this disease is cat. By ECD MS/MS, a substitution of Asp7 → Glu in cat Aβ was identified. Further, sialylated core 1 like O-glycans at Tyr10, recently discovered in human Aβ (a previously unknown glycosylation type), were identified also in cat cerebrospinal fluid (CSF). It is therefore likely that this unusual type of glycosylation is common for (at least) species belonging to the magnorder Boreoeutheria. We here describe a detailed characterization of endogenous APP/Aβ peptide species in CSF by using an online top-down MS-based method.

Electrospray tandem mass spectrometric analysis of duboscic acid, exploring the structural features of a new class of triterpenoids, dubosane

Duboscic acid belongs to a new class of triterpenoids dubosane, isolated from Duboscia macrocarpa. Gas-phase fragmentation of duboscic acid was studied using positive ion electrospray ionization quadropole time-of-flight mass spectrometry (ESI-QqTOF-MS/MS) hybrid instrument. ESI-QqTOF-MS (positive ion mode) showed the presence of the protonated molecule [M+H] + which under low-energy collision-induced dissociation tandem mass spectrometric (CID-MS/MS) analysis showed the characteristic losses of methoxy, hydroxyl and carboxylic groups. Our results demonstrated the characteristic fragments of this new class of triterpenoids which are formed due to the cleavage of seven membered unsaturated ring C. The fragmentation pathways of characteristic fragments were proposed with the aid of HRMS and computational studies. The knowledge of the fragmentation pattern and key fragment ions of duboscic acid, i.e. gas phase fragmentation behavior of unique dubosane structure, will be useful for further exploration of the related species of the same genera for the characterization of novel members of this class of compounds.

Rapid characterization and identification of steroidal alkaloids in Sarcococca coriacea using liquid chromatography coupled with electrospray ionization quadropole time-of-flight mass spectrometry

Rapid characterization of 23 pregnane-type steroidal alkaloids was studied using a positive ion electrospray ionization quadropole time-of-flight mass spectrometry (ESI-QqTOF–MS/MS) hybrid instrument. ESI-QqTOF–MS (positive ion mode) showed the presence of the protonated molecules [M+H] + which through low-energy collision-induced dissociation tandem mass spectrometric (CID–MS/MS) analysis showed the characteristic loss of dimethylamine moiety [M+H-45] + followed by the sequential lossess of attached substituents. Steroidal alkaloids having tigloyl or senecioyl group at C-3 produced diagnostic fragment ions at m/ z 100 and 83. Our study also demonstrates the influence of unsaturation, and number and nature of substitutents on product ion abundance and fragment ions. Moreover, the generalization of the fragmentation pattern was linked with the structural features in steroidal skeleton. This strategy was successfully applied in LC–ESI-QqTOF–MS/MS analysis of Sarcococca coriacea extract to investigate and characterize pregnane-type steroidal alkaloids in complex mixture.

Analysis and development of structure‐fragmentation relationships in withanolides using an electrospray ionization quadropole time‐of‐flight tandem mass spectrometry hybrid instrument

Structural elucidation and gas-phase fragmentation of ten withanolides (steroidal lactones) were studied using a positive ion electrospray ionization quadropole time-of-flight mass spectrometry (ESI-QqTOF-MS/MS) hybrid instrument. Withanolides form an important class of plant secondary metabolites, known to possess a variety of biological activities. Withanolides which possess hydroxyl groups at C-4, C-5, C-17, C-20, and C-27, and an epoxy group at C-5/C-6, were evaluated to determine the characteristic fragments and their possible pathways. ESI-QqTOF-MS (positive ion mode) showed the presence of the protonated molecules [M + H](+) . Low-energy collision-induced dissociation tandem mass spectrometric (CID-MS/MS) analysis of the protonated molecule [M + H](+) indicated multiple losses of water and the removal of the C-17-substituted lactone moiety affording the [M + H-Lac](+) product ion as the predominant pathways. However, withanolides containing a hydroxyl group at C-24 of the lactone moiety showed a different fragmentation pathway, which include the loss of steroidal part as a neutral molecule, with highly diagnostic ions at m/z 95 and 67 being generated from the cleavage of lactone moiety. Our results also determined the influence of the presence and positions of hydroxyl and epoxy groups on product ion formation and stability. Moreover, the knowledge of the fragmentation pattern was utilized in rapid identification of withanolides by the LC/MS/MS analysis of a Withania somnifera extract.

A novel approach for quantitative peptides analysis by selected electron transfer reaction monitoring

Liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) with selective reaction monitoring (SRM) is a selective and sensitive method for quantitation of peptides. SRM is achieved via MS/MS utilizing collision-induced dissociation (CID) while monitoring unique precursor-product ion transitions. Low-energy CID tandem mass spectrometry has been, by far, the most common method used to dissociate peptide ions for sequence analysis. However, collisional scattering of product ions in CID results in decreased intensity of the primary product ion. The lower intensity of the targeted product ion can lead to a reduction in the sensitivity of a quantitative method that uses SRM. Electron transfer dissociation (ETD) is a fragmentation method that is complementary to CID. During the ETD reaction for doubly protonated peptides ([M+2H] 2+), there is a significant shift toward nondissociative electron transfer (ET) product species ([M+2H] + ). We utilized that particular defect in ETD to develop a new quantitative method for monitoring the transition of unique precursors ([M+2H] 2+) to charge-reduced ions ([M+2H] + ). We refer to this method as selective electron transfer reaction monitoring (SETRM). In ESI-MS, trypsin-digested peptides tend to generate doubly protonated peptide precursors. We found that SETRM was more suitable than SRM for these doubly charged tryptic peptides with nano-LC–MS/MS. The quantitative capabilities of SETRM provide a more sensitive way of performing quantitative experiments using the same instrument, thereby improving the application of electron transfer dissociation in proteomics.

Determination and quantification of active phenolic compounds in pigeon pea leaves and its medicinal product using liquid chromatography–tandem mass spectrometry

A novel method using liquid chromatography coupled to electrospray ionization mass spectrometry (LC–ESI-MS) has been optimized and established for the qualitative and quantitative analysis of ten active phenolic compounds originating from the pigeon pea leaves and a medicinal product thereof (Tongluo Shenggu capsules). In the present study, the chromatographic separation was achieved by means of a HiQ Sil C18 V reversed-phase column with a mobile phase consisting of methanol and 0.1% formic acid aqueous solution. Low-energy collision-induced dissociation tandem mass spectrometry (CID-MS/MS) using the selected reaction monitoring (SRM) analysis was employed for the detection of ten analytes which included six flavonoids, two isoflavonoids and two stilbenes. All calibration curves showed excellent coefficients of determination ( r 2 ≥ 0.9937) within the range of tested concentrations. The intra- and inter-day variations were below 5.36% in terms of relative standard deviation (RSD). The recoveries were 95.08–104.98% with RSDs of 2.06–4.26% for spiked samples of pigeon pea leaves. The method developed was a rapid, efficient and accurate LC–MS/MS method for the detection of phenolic compounds, which can be applied for quality control of pigeon pea leaves and related medicinal products.

Screening for Anticoagulant Heparan Sulfate Octasaccharides and Fine Structure Characterization Using Tandem Mass Spectrometry

Heparan sulfate (HS) is a sulfated glycosaminoglycan located on the surface and extracellular matrix of mammalian cells. HS is constituted of highly N-sulfated domains (NS domains) interrupted by lower sulfation domains. The arrangement of these domains dictates the function of HS which is mainly involved in binding proteins and regulating their biological activities. Heparin, a heparan sulfate analogue present in mast cells, resembles the NS domains of HS but lacks the alternating high and low sulfation architecture. Because the NS domains that range up to hexadecasaccharide in size are the main protein binders, heparin has been used as a model for HS in protein binding studies. Heparan sulfate, however, is the more physiologically relevant modulator of growth factor-receptor interactions. In this work, liquid chromatography and mass spectrometry (LC-MS) were used to compare the compositions of affinity-purified heparin and HS octasaccharides with anticoagulant activities versus library octasaccharides. The fine structures of the biologically active HS compositions were then compared against those of library octasaccharides using low-energy collision-induced dissociation tandem mass spectrometry. This approach confirmed isomeric enrichment of these compositions and, most importantly, produces ions diagnostic of their biological activity.

Study on the matrix effect in the determination of selected pharmaceutical residues in seawater by solid-phase extraction and ultra-high-performance liquid chromatography–electrospray ionization low-energy collision-induced dissociation tandem mass spectrometry

Matrix effect is a major problem when trace level pharmaceuticals in seawater were analyzed using solid-phase extraction (SPE) combined with high-performance liquid chromatography–electrospray ionization tandem mass spectrometry (HPLC–ESI–MS–MS). Therefore, efforts should be devoted to diminish matrix effect as much as possible. The present study investigates the matrix effect during the analysis of selected pharmaceutical residues (naproxen, ibuprofen, diclofenac and gemfibrozil) in seawater samples with ultra-high-performance liquid chromatography (UHPLC)–ESI low-energy collision-induced dissociation (CID) MS–MS. Solutions to reduce matrix effect were studied through optimization of SPE procedure and the employment of isotope-labeled analogues. Results showed that 30 mL of deionized water can efficiently diminish matrix effect and satisfactory absolute mean recoveries ranging from 73.5% to 120.5% were obtained in the optimized SPE condition. Isotope-labeled analogues employed as surrogates were found to be efficient to further compensate for matrix effect, with the relative mean recoveries ranging from 85.5% to 110.5%. The optimized method has been successfully applied for the analysis of target pharmaceutical residues in different seawater samples.

Determination of para-aminohippuric acid (PAH) in human plasma and urine by liquid chromatography–tandem mass spectrometry

In this manuscript, we present a simple and reliable method for the quantitation of para-aminohippuric acid (PAH; 2-(4-aminobenzamido)acetic acid) in human plasma and urine using liquid chromatography coupled to electrospray ionisation low-energy collision-induced dissociation tandem mass spectrometry (HPLC–ESI-CID-MS/MS) analysis (negative ion mode) via multiple reaction monitoring (MRM). Sample preparation involved protein precipitation of plasma samples with acetonitrile and subsequent dilution of urine samples with the mobile phase. The internal standard (IS) adopted was para-aminosalicylic acid (PAS; 4-amino-2-hydroxybenzoic acid). Chromatographic separation was achieved on a Cosmosil HILIC column using an isocratic mobile phase consisting of ammonium acetate buffer (20 mM) and acetonitrile (45:55, v/v) at a flow rate of 200 μl/min. The transactions monitored were m/ z 192.9 → 149.1 for PAH and m/ z 152.1 → 108.1 for IS. Linear calibration curves were generated over the PAH concentration range of 0.2–100 mg/L in human plasma and urine. The method was validated for selectivity, accuracy, precision, recovery and stability according to USFDA criteria, and has been successfully applied to a pharmacokinetic study in healthy volunteers administered an intravenous dose of 440 mg PAH.