Tandem Mass Spectrometry Experiments Research Articles

Mass spectrometric characterization of aminophospholipids containing N-(2-hydroxyethyl)glycine in kombu algae extracts.

1,2-Diacyl-sn-glycero-3-phospho-O-[N-(2-hydroxyethyl)glycines] (PHEGs) are a class of rare aminophospholipids found specifically in brown algae, including kombu seaweed. Despite their potential importance in algal physiology, a comprehensive mass spectrometry (MS) characterization, useful to understand their biological behaviour, is still lacking. To establish the structural regiochemical features of PHEGs, we employed hydrophilic interaction liquid chromatography (HILIC). Following separation, the isolated band of PHEGs was analyzed using MS techniques. This included multistage tandem MS experiments, performed in both positive and negative electrospray ionization modes at low and high resolution. By comparing MS/MS and MS3 spectra acquired in negative ion mode, the regiochemical rules for PHEG identification were established. The most abundant PHEG species in kombu seaweed, from both Laminaria ochroleuca (European Atlantic) and Laminaria longissima (Japan), was identified as PHEG 20:4/20:4. Less abundant species included PHEG 20:4/20:5 and hydroxylated forms of both PHEG 20:4/20:4 (i.e. 40:8;O) and 20:4/20:5 (40:9;O). The presence of a lyso PHEG 20:4 was consistently detected but at very low levels. This study employed MS analysis to elucidate the regiochemical patterns of PHEGs in kombu seaweed. We identified PHEG 20:4/20:4 as the dominant species, along with several less abundant variants, including hydroxylated forms. These findings provide valuable insights into the potential roles and metabolism of PHEGs in brown algae, paving the way for further investigation into their biological functions.

Removal of isobaric interference using pseudo-multiple reaction monitoring and energy-resolved mass spectrometry for the isotope dilution quantification of a tryptic peptide.

Energy-resolved mass spectrometry (ERMS) and an isotopically labelled internal standard were successfully combined to accurately quantify a tryptic peptide despite the presence of an isobaric interference. For this purpose, electrospray ionisation tandem mass spectrometry (ESI-MS/MS) experiments were conducted into an ion trap instrument using an unconventional 8m/z broadband isolation window, which encompassed both the tryptic peptide and its internal standard. Interference removal was assessed by determining an excitation voltage that was high enough to maintain a constant value for the analyte/internal standard peaks intensity ratio, thus ensuring accurate quantification even in the presence of isobaric contamination. Pseudo-multiple reaction monitoring (MRM) was employed above this excitation voltage to quantify the trypic peptide. The internal standard calibration model showed no lack of fit and exhibited a linear dynamic range from 0.5μM up to 2.5μM. The detection limit was 0.08 μM. The accuracy of the method was evaluated by quantifying the tryptic peptide of three reference samples intentionally contaminated with the isobaric interference. All the reference samples were accurately quantified with ∼1% deviation despite the isobaric contamination. Furthermore, we have demonstrated that this methodology can also be applied to quantify the isobaric peptide by standard additions down to 0.2μM. Finally, liquid chromatography ERMS (LC ERMS) experiments yielded similar results, suggesting the potential of the proposed methodology for analysing complex samples.

Identification and characterization of impurities in an insecticide, commercial chlorantraniliprole using liquid chromatography-tandem mass spectrometry.

Ensuring the global safety and effectiveness of agrochemicals has become imperative. An in-depth understanding of impurity profiles of products is crucial, especially for high-demand agrochemicals, where impurities may be more toxic and persistent than original agrochemicals. This study focuses on the detection and identification of impurities in a commercial chlorantraniliprole (CAP), an anthranilic diamide class broad-spectrum insecticide. Commercial CAP was collected from an agrochemical supplier in India and was analyzed using a high-performance liquid chromatography-photodiode array (HPLC-PDA) (Agilent 1260; wavelength, 220 nm) with a Zorbax RP SB-C18 (250 × 4.6mm, 5μm) column and liquid chromatography-mass spectrometry (LC-MS) (Agilent 6545 quadrupole time of flight (Q-TOF)) techniques to identify the impurities. The impurities were isolated by preparative HPLC using a Zorbax-DB C18 (250 × 9.4mm, 5μm) column. liquid chromatography- tandem mass spectrometry (LC-MS/MS) experiments (Q-TOF) were performed on CAP and its impurities to obtain their structural data. HPLC-PDA analysis of CAP showed four major impurities (IM-1 to IM-4) ranging from 0.76% to 4.1%. The positive ion electrospray ionization (ESI) mass spectra of CAP and its impurities showed dominant [M + H]+ ions in addition to [M + Na]+ , [M + K]+ , and [2M + Na]+ ions. High-resolution mass spectrometry (HRMS) data provided the elemental composition of the compounds, and isotopic distribution patterns revealed the number of Cl and/or Br atoms present in them. The structures of impurities were proposed based on the LC-MS/MS) data and further confirmed by nuclear magnetic resonance (NMR) data on isolated impurities/synthesis. The quality and impurities of CAP, a popular insecticide, must be assessed and described for its efficacy and safety. In this study, four impurities of CAP were detected using HPLC and successfully characterized using LC-HRMS, LC-MS/MS, and NMR data. The method is useful for verifying the purity of CAP as well as helping in the identification of its possible impurities.

MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.

Although many user-friendly workflows exist for identifications of peptides and proteins in mass-spectrometry-based proteomics, there is a need of easy to use, fast, and accurate workflows for identifications of microorganisms, antimicrobial resistant proteins, and biomass estimation. Identification of microorganisms is a computationally demanding task that requires querying thousands of MS/MS spectra in a database containing thousands to tens of thousands of microorganisms. Existing software can't handle such a task in a time efficient manner, taking hours to process a single MS/MS experiment. Another paramount factor to consider is the necessity of accurate statistical significance to properly control the proportion of false discoveries among the identified microorganisms, and antimicrobial-resistant proteins, and to provide robust biomass estimation. Recently, we have developed Microorganism Classification and Identification (MiCId) workflow that assigns accurate statistical significance to identified microorganisms, antimicrobial-resistant proteins, and biomass estimation. MiCId's workflow is also computationally efficient, taking about 6-17 minutes to process a tandem mass-spectrometry (MS/MS) experiment using computer resources that are available in most laptop and desktop computers, making it a portable workflow. To make data analysis accessible to a broader range of users, beyond users familiar with the Linux environment, we have developed a graphical user interface (GUI) for MiCId's workflow. The GUI brings to users all the functionality of MiCId's workflow in a friendly interface along with tools for data analysis, visualization, and to export results.

Characterization of phytochemicals from twisted-leaf garlic (Allium obliquum L.) using liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry

IntroductionTwisted-leaf garlic (Allium obliquum L.) is a wild Allium species, which is traditionally used as aroma plant for culinary purposes due to its unique, garlic-like flavor. It represents an interesting candidate for domestication, breeding and cultivation.ObjectivesThe objective of this work was to explore and comprehensively characterize polar and semi-polar phytochemicals accumulating in leaves and bulbs of A. obliquum.MethodPlant material obtained from a multiyear field trial was analyzed using a metabolite profiling workflow based on ultra-high performance liquid chromatography-coupled electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC/ESI-QTOFMS) and two chromatographic methods. For annotation of metabolites, tandem mass spectrometry experiments were carried out and the resulting accurate-mass collision-induced dissociation (CID) mass spectra interpreted. Onion and garlic bulb extracts were used as reference samples.ResultsImportant metabolite classes influencing nutritional, sensory and technological properties were detected and structurally characterized including fructooligosaccharides with a degree of polymerization of 3–5, S-alk(en)ylcysteine sulfoxides and other S-substituted cysteine conjugates, flavonoids including O- and C-glycosylated flavones as well as O-glycosylated flavonols, steroidal saponins, hydroxycinnamic acid conjugates, phenylethanoids and free sphingoid bases. In addition, quantitative data for non-structural carbohydrates, S-alk(en)ylcysteine sulfoxides and flavonoids are provided.ConclusionThe compiled analytical data including CID mass spectra of more than 160 annotated metabolites provide for the first time a phytochemical inventory of A. obliquum and lay the foundation for its further use as aroma plant in food industry.

Large-scale Bioinformatic Study of Graspimiditides and Structural Characterization of Albusimiditide.

Graspetides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that exhibit an impressive diversity in patterns of side chain-to-side chain ω-ester or ω-amide linkages. Recent studies have uncovered a significant portion of graspetides to contain an additional post-translational modification involving aspartimidylation catalyzed by an O-methyltransferase, predominantly found in the genomes of actinomycetota. Here, we present a comprehensive bioinformatic analysis focused on graspetides harboring aspartimide, for which we propose the name graspimiditides. From protein BLAST results of 5000 methyltransferase sequences, we identified 962 unique putative graspimiditides, which we further classified into eight main clusters based on sequence similarity along with several smaller clusters and singletons. The previously studied graspimiditides, fuscimiditide, and amycolimiditide, are identified in this analysis; fuscimiditide is a singleton, while amycolimiditide is in the fifth largest cluster. Cluster 1, by far the largest cluster, contains 641 members, encoded almost exclusively in the Streptomyces genus. To characterize an example of a graspimiditide in Cluster 1, we conducted experimental studies on the peptide from Streptomyces albus J1074, which we named albusimiditide. By tandem mass spectrometry, hydrazinolysis, and amino acid substitution experiments, we elucidated the structure of albusimiditide to be a large tetracyclic peptide with four ω-ester linkages generating a stem-loop structure with one aspartimide. The ester cross-links form 22-, 46-, 22-, and 44-atom macrocycles, the last of which, the loop, contains the enzymatically installed aspartimide. Further in vitro experiments revealed that the aspartimide hydrolyzes in a 3:1 ratio of isoaspartate to aspartate residues. Overall, this study offers comprehensive insight into the diversity and structural features of graspimiditides, paving the way for future investigations of this unique class of natural products.

Chemical Exposure Highlighted without Any A Priori Information in an Epidemiological Study by Metabolomic FT-ICR-MS Fingerprinting at High Throughput and High Resolution.

Epidemiological studies aim to assess associations between diseases and risk factors. Such investigations involve a large sample size and require powerful analytical methods to measure the effects of risk factors, resulting in a long analysis time. In this study, chemical exposure markers were detected as the main variables strongly affecting two components coming from a principal component analysis (PCA) exploration of the metabolomic data generated from urinary samples collected on a cohort of about 500 individuals using direct introduction coupled with a Fourier-transform ion cyclotron resonance instrument. The assignment of their chemical identity was first achieved based on their isotopic fine structures detected at very high resolution (Rp > 900,000). Their identification as dimethylbiguanide and sotalol was obtained at level 1, thanks to the available authentic chemical standards, tandem mass spectrometry (MS/MS) experiments, and collision cross section measurements. Epidemiological data confirmed that the subjects discriminated by PCA had declared to be prescribed these drugs for either type II diabetes or cardiac arrhythmia. Concentrations of these drugs in urine samples of interest were also estimated by rapid quantification using an external standard calibration method, direct introduction, and MS/MS experiments. Regression analyses showed a good correlation between the estimated drug concentrations and the scores of individuals distributed on these specific PCs. The detection of these chemical exposure markers proved the potential of the proposed high-throughput approach without any prior drug exposure knowledge as a powerful emerging tool for rapid and large-scale phenotyping of subjects enrolled in epidemiological studies to rapidly characterize the chemical exposome and adherence to medical prescriptions.

Paper spray mass spectrometry profiling of olive oil unsaponifiable fraction for commercial categories classification

A new method for a fast molecular profiling of olive oil unsaponifiable fraction has been developed. This approach, based on paper spray mass spectrometry, allows obtaining MS data with only a few minutes of analysis and without significant solvent and disposable consumption. Tandem mass spectrometry and high-resolution mass spectrometry experiments have been performed to identify the main ions detected. The MS data coming from the analyses of sixty-three samples of three different olive oil categories: extra virgin olive oil (EVOO), virgin olive oil (VOO), and pomace olive oil (POO), have been used to test the discriminative potential. Both unsupervised (PCA and HCA) and supervised (kNN and LDA) chemometric procedures have been applied with good results in prediction. The same approach was tested using direct infusion mass spectrometry data to confirm the ability of paper spray fingerprinting to classify different olive oils correctly.

Top-Down Protein Analysis by Tandem-Trapped Ion Mobility Spectrometry/Mass Spectrometry (Tandem-TIMS/MS) Coupled with Ultraviolet Photodissociation (UVPD) and Parallel Accumulation/Serial Fragmentation (PASEF) MS/MS Analysis.

"Top-down" proteomics analyzes intact proteins and identifies proteoforms by their intact mass as well as the observed fragmentation pattern in tandem mass spectrometry (MS/MS) experiments. Recently, hybrid ion mobility spectrometry-mass spectrometry (IM/MS) methods have gained traction for top-down experiments, either by allowing top-down analysis of individual isomers or alternatively by improving signal/noise and dynamic range for fragment ion assignment. We recently described the construction of a tandem-trapped ion mobility spectrometer/mass spectrometer (tandem-TIMS/MS) coupled with an ultraviolet (UV) laser and demonstrated a proof-of-principle for top-down analysis by UV photodissociation (UVPD) at 2-3 mbar. The present work builds on this with an exploration of a top-down method that couples tandem-TIMS/MS with UVPD and parallel-accumulation serial fragmentation (PASEF) MS/MS analysis. We first survey types and structures of UVPD-specific fragment ions generated in the 2-3 mbar pressure regime of our instrument. Notably, we observe UVPD-induced fragment ions with multiple conformations that differ from those produced in the absence of UV irradiation. Subsequently, we discuss how MS/MS spectra of top-down fragment ions lend themselves ideally for probability-based scoring methods developed in the bottom-up proteomics field and how the ability to record automated PASEF-MS/MS spectra resolves ambiguities in the assignment of top-down fragment ions. Finally, we describe the coupling of tandem-TIMS/MS workflows with UVPD and PASEF-MS/MS analysis for native top-down protein analysis.

Real-Time Mass Spectrometric Detection of Reaction Intermediates Formed during Laser-Induced UV/H2O2 Advanced Oxidation of 2-Methylbenzoisothiazol-3-one.

Knowledge on short-lived reaction intermediates is often essential for mechanistic investigations of organic reactions and for reaction optimization. Unfortunately, most conventional analytical methods are too slow to allow the detection of short-lived reaction intermediates. Herein, a direct laser desorption/ionization method coupled with linear quadrupole ion trap/orbitrap high-resolution tandem mass spectrometry was used for the detection and structural characterization of several previously proposed but undetected reaction intermediates formed during laser-induced UV/H2O2 advanced oxidation of 2-methylbenzoisothiazol-3-one. The elemental compositions of most detected (ionized) compounds were determined. Tandem mass spectrometry experiments based on gas-phase collision-activated dissociation (CAD) were conducted to gain information on the ion structures. The mechanisms of the CAD reactions were explored using high-level quantum chemical calculations to support the structures proposed for the neutral reaction intermediates formed during the laser-induced UV/H2O2 advanced oxidation of 2-methylbenzoisothiazol-3-one. In the negative-ion mode experiments, anions corresponding to three reaction intermediates were detected and structurally characterized: 1-hydroxy-2-methyl-1,2-dihydro-3H-1λ4-benzo[d]isothiazol-3-one, 2-(methylcarbamoyl)benzenesulfinic acid, and 2-(dihydroxy(oxo)-λ6-sulfaneyl)-N-methylbenzamide. One of the final products, 2-(methylcarbamoyl)benzenesulfonic acid, was also detected and characterized. In positive-ion mode experiments, cations corresponding to the reactant, 2-methylbenzoisothiazol-3-one, as well as an intermediate reaction product and the two final reaction products, 2-methylbenzo[d]isothiazol-3(2H)-one 1-oxide, N-methylsaccharine, and 2-(methylcarbamoyl)benzenesulfonic acid, respectively, were detected and identified. This research substantially improved the understanding on the reaction intermediates formed during laser-induced UV/H2O2 advanced oxidation of 2-methylbenzoisothiazol-3-one, which facilitates the delineation of the reaction mechanisms occurring in these processes.

TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments.

Liquid Chromatography Tandem Mass Spectrometry experiments aim to produce high-quality fragmentation spectra, which can be used to annotate metabolites. However, current Data-Dependent Acquisition approaches may fail to collect spectra of sufficient quality and quantity for experimental outcomes, and extend poorly across multiple samples by failing to share information across samples or by requiring manual expert input. We present TopNEXt, a real-time scan prioritization framework that improves data acquisition in multi-sample Liquid Chromatography Tandem Mass Spectrometry metabolomics experiments. TopNEXt extends traditional Data-Dependent Acquisition exclusion methods across multiple samples by using a Region of Interest and intensity-based scoring system. Through both simulated and lab experiments, we show that methods incorporating these novel concepts acquire fragmentation spectra for an additional 10% of our set of target peaks and with an additional 20% of acquisition intensity. By increasing the quality and quantity of fragmentation spectra, TopNEXt can help improve metabolite identification with a potential impact across a variety of experimental contexts. TopNEXt is implemented as part of the ViMMS framework and the latest version can be found at https://github.com/glasgowcompbio/vimms. A stable version used to produce our results can be found at 10.5281/zenodo.7468914.

Molecular Characterization of Brown Carbon Chromophores in Atmospherically Relevant Samples and Their Gas‐Particle Distribution and Diurnal Variation in the Atmosphere

AbstractBy developing a nontarget tandem mass spectrometry experiment workflow, we identified the most probable structures of 100 brown carbon (BrC) chromophores in five types of atmospherically relevant samples including ambient aerosols, biomass burning aerosols, road tunnel aerosols, toluene secondary organic aerosol and rainwater. These chromophores were classified into nine groups, that is, 31 nitrophenols, 12 benzoic acids, 11 oxygenated polycyclic aromatic hydrocarbons, 10 phenols, 10 aryl amides/amines, 9 phenylpropene derivatives, 9 coumarins and flavonoids, 5 pyridines, and 3 nitrobenzoic acids. Among them, aryl amides/amine chromophores, which were mostly found in rainwater, were reported for the first time. The identified chromophores accounted for 20.9%–83.5% of total light absorption over 300–400 nm wavelength or total ion intensity in the 5 types of samples. We identified the characteristic chromophore groups in each sample type and identical chromophores among different sample types, especially between the source samples and ambient aerosols. Gas‐particle distribution and diurnal variation of 13 BrC compounds in the atmosphere were measured by an online high‐resolution chemical ionization mass spectrometer equipped with a Filter Inlet for Gases and Aerosols. It was found that gas‐particle distribution of BrC compounds was dictated by their functional group, oxygen and carbon atom numbers. The BrC compounds containing nitro‐group had higher nighttime concentrations, while those without nitro‐group had higher daytime concentrations.

Evaluation of Tandem Mass Spectrometry Experiments in the Negative Ionization Mode for Phenolamide Regioisomer Characterization.

Phenolamides are abundant specialized metabolites found in nature and consist of hydroxycinnamic acids mono- or polyconjugated with polyamines. Their participation in flower development is well-documented, and their presence in pollen raises the question of their role in pollen/pollinator interactions. The structural characterization of phenolamides is complicated by the presence of positional isomers and stereoisomers. Liquid chromatography coupled to tandem mass spectrometry in the positive ionization mode is becoming very popular in phenolamide structural characterization. However, collision-induced transamidation processes that cause the swapping of side chains have been detected, making it difficult to distinguish regioisomers with this technique. In the present report, we explore the dissociation processes undergone by the [M - H]- ions of spermidine-based phenolamides as model compounds. We describe two original competitive dissociation routes, namely, the phenolate and imidate pathways, to account for the observed fragmentation reactions undergone by collisional activated standard phenolamide anions. Whereas the phenolate pathway is regioselective at the central position for spermidine, the imidate pathway, requiring a deprotonated amide, only occurs at the extremities. Tandem mass spectrometry experiments on negatively charged phenolamide ions may then outperform their positive ionization mode counterparts for the distinction between phenolamide regioisomers and globally for the identification of phenolamides in natural extracts.

Expanding Orbitrap Collision Cross-Section Measurements to Native Protein Applications Through Kinetic Energy and Signal Decay Analysis.

The measurement of collision cross sections (CCS, σ) offers supplemental information about sizes and conformations of ions beyond mass analysis alone. We have previously shown that CCSs can be determined directly from the time-domain transient decay of ions in an Orbitrap mass analyzer as ions oscillate around the central electrode and collide with neutral gas, thus removing them from the ion packet. Herein, we develop the modified hard collision model, thus deviating from the prior FT-MS hard sphere model, to determine CCSs as a function of center-of-mass collision energy in the Orbitrap analyzer. With this model, we aim to increase the upper mass limit of CCS measurement for native-like proteins, characterized by low charge states and presumed to be in more compact conformations. We also combine CCS measurements with collision induced unfolding and tandem mass spectrometry experiments to monitor protein unfolding and disassembly of protein complexes and measure CCSs of ejected monomers from protein complexes.

MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics

Posttranslational modifications of proteins play essential roles in defining and regulating the functions of the proteins they decorate, making identification of these modifications critical to understanding biology and disease. Methods for enriching and analyzing a wide variety of biological and chemical modifications of proteins have been developed using mass spectrometry-based proteomics, largely relying on traditional database search methods to identify the resulting mass spectra of modified peptides. These database search methods treat modifications as static attachments of a mass to particular position in the peptide sequence, but many modifications undergo fragmentation in tandem mass spectrometry experiments alongside, or instead of, the peptide backbone. While this fragmentation can confound traditional search methods, it also offers unique opportunities for improved searches that incorporate modification-specific fragment ions. Here, we present a new labile mode in the MSFragger search engine that provides the flexibility to tailor modification-centric searches to the fragmentation observed. We show that labile mode can dramatically improve spectrum identification rates of phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides. Each of these modifications presents distinct fragmentation characteristics, showcasing the flexibility of MSFragger labile mode to improve search for a wide variety of biological and chemical modifications.

α-Dicarbonyl compounds trapping ability and antiglycative effect of high-molecular-weight brewer's spent grain melanoidins

Polyphenols participate in the Maillard reaction pathways scavenging α-dicarbonyl compounds (DCs) and contributing to the mitigation of carbonyl burden through dietary exposure/routes. The current study demonstrated the effectiveness of high-molecular-weight brewer's spent grain melanoidins (HMW-BSGM) in reacting with DCs in an in vitro model system. HMW-BSGM (4 mg/mL) quenched more than 95% of glyoxal and methylglyoxal, and more than 80% of 2,3-butanedione after a 7-day incubation at 37 °C. Among tested polyphenols, sinapic acid showed the highest trapping capacity with inhibition rates of 33.1, 49.1 and 49.3% for glyoxal, methylglyoxal and 2,3-butanedione because of hydroxyalkylation reaction as revealed by liquid chromatography high-resolution tandem mass spectrometry experiments. The formation of free fluorescent AGEs was substantially hindered (79.3%) by HMW-BSGM (4 mg/mL). These findings corroborate the hypothesis that the accumulation of polyphenols in melanoidins skeleton can hinder undesired effects and potentially harmful reactions involving α-dicarbonyl compounds.

Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations.

Biomass-derived degraded lignin and cellulose serve as possible alternatives to fossil fuels for energy and chemical resources. Fast pyrolysis of lignocellulosic biomass generates bio-oil that needs further refinement. However, as pyrolysis causes massive degradation to lignin and cellulose, this process produces very complex mixtures. The same applies to degradation methods other than fast pyrolysis. The ability to identify the degradation products of lignocellulosic biomass is of great importance to be able to optimize methodologies for the conversion of these mixtures to transportation fuels and valuable chemicals. Studies utilizing tandem mass spectrometry have provided invaluable, molecular-level information regarding the identities of compounds in degraded biomass. This review focuses on the molecular-level characterization of fast pyrolysis and other degradation products of lignin and cellulose via tandem mass spectrometry based on collision-activated dissociation (CAD). Many studies discussed here used model compounds to better understand both the ionization chemistry of the degradation products of lignin and cellulose and their ions' CAD reactions in mass spectrometers to develop methods for the structural characterization of the degradation products of lignocellulosic biomass. Further, model compound studies were also carried out to delineate the mechanisms of the fast pyrolysis reactions of lignocellulosic biomass. The above knowledge was used to assign likely structures to many degradation products of lignocellulosic biomass.

MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search

Spectral library search can enable more sensitive peptide identification in tandem mass spectrometry experiments. However, its drawbacks are the limited availability of high-quality libraries and the added difficulty of creating decoy spectra for result validation. We describe MS Ana, a new spectral library search engine that enables high sensitivity peptide identification using either curated or predicted spectral libraries as well as robust false discovery control through its own decoy library generation algorithm. MS Ana identifies on average 36% more spectrum matches and 4% more proteins than database search in a benchmark test on single-shot human cell-line data. Further, we demonstrate the quality of the result validation with tests on synthetic peptide pools and show the importance of library selection through a comparison of library search performance with different configurations of publicly available human spectral libraries.

Carfentanil structural analogs found in street drugs by paper spray mass spectrometry and their characterization by high-resolution mass spectrometry.

Carfentanil is one of the most potent synthetic opioids ever developed, with an estimated analgesic potency approximately 20-100 times that of fentanyl and 10,000 times that of morphine. Carfentanil has been appearing in the illicit drug supply in many regions and has been linked to fatal overdose events. A subset of 59 street drug samples obtained in Victoria, B.C., that were confirmed to contain carfentanil were analyzed by mass spectrometry for this study. Carfentanil quantitation by paper spray mass spectrometry ranged from 0.05 to 2.95 w/w% (median =0.32%) in the original drug sample. Paper spray mass spectrometry analysis also detected two unknown peaks at m/z 380.2 and 381.2 in 31 of these 59 samples (53%). Initial tandem mass spectrometry experiments revealed structural similarities between these unknown compounds and carfentanil, suggesting they were potential structural analogs, possibly arising from incomplete purification during synthesis. High-resolution mass spectrometry determined the chemical formulas of these compounds as C23 H29 N3 O2 (m/z 380.2333) and C23 H29 N2 O3 (m/z 381.2137). Literature and tandem mass spectrometry results were used to determine the identity of these potential new psychoactive substances, C23 H29 N3 O2 as desmethylcarfentanil amide and C23 H29 N2 O3 as desmethylcarfentanil acid. μ-Opioid receptor binding modeling determined that the binding poses of these analogs were nearly identical to that of carfentanil with relative binding energy calculations of 0.544 kJ/mol (desmethylcarfentanil amide) and -0.171 kJ/mol (desmethylcarfentanil acid); these data suggest they may share the toxic effects of carfentanil and have similar potencies.

Mobility-resolved broadband dissociation and parallel reaction monitoring for laser desorption/ionization-mass spectrometry - Tattoo pigment identification supported by trapped ion mobility spectrometry

In this work, trapped ion mobility spectrometry (TIMS) was introduced to facilitate tandem mass spectrometry (MS2) experiments for laser desorption/ionization-mass spectrometry (LDI-MS) as mobility-resolved fragmentation. The mobility separation of desorbed ions was followed by subsequent fragmentation using data-independent broadband collision-induced dissociation (bbCID) or targeted fragmentation through a prototypic version of parallel reaction monitoring-parallel accumulation serial fragmentation (prm-PASEF) for LDI. Both mobility-resolved fragmentation options, TIMS-bbCID and prm-PASEF, were applied to LDI point measurements to identify organic pigments in tattoo inks. Furthermore, the prototypic prm-PASEF algorithm was used in imaging applications to increase confidence in annotating organic tattoo pigments in skin samples with adverse reactions. Due to less complex spectra in matrix-free LDI, both fragmentation methods yielded fast and reliable MS2 identification workflows. TIMS-bbCID was especially beneficial for the rapid acquisition of multiple fragment spectra. For the targeted prm-PASEF approach, analytes’ mobilities needed to be collected prior to simplified fragmentation. Therefore, a reference list for 14 pigments was created. The possible number of experiments per thin section and the associated savings in analysis time compared to conventional MS2 were particularly suitable for the imaging application. Furthermore, the mobility dimension enabled a new orthogonal identification parameter, increasing the annotation confidence of tattoo pigments through compound specific mobilities.