Single Mass Spectrum Research Articles

A biological reading of a palimpsest

In the Middle Ages, texts were recorded and preserved on parchment, an animal-derived material. When this resource was scarce, older manuscripts were sometimes recycled to write new manuscripts. In the process, the ancient text was erased, creating what is known as a palimpsest. Here, we explore the potential of peptide mass fingerprinting (PMF), widely applied to identify species, to help reconnect the dispersed leaves of a manuscript and reveal differences in parchment manufacturing. In combination with visual methods, we analyzed a whole palimpsest, the codex AM 795 4to from the Arnamagnæan Collection (Copenhagen, Denmark). We find that both sheep and goat skins were used in this manuscript, and that parchment differed in quality. Notably, the PMF analysis distinguished five groups of folios which match the visual groupings. We conclude that this detailed interrogation of a single mass spectrum can be a promising tool to understand how palimpsest manuscripts were constructed.

PyC2MC: An Open-Source Software Solution for Visualization and Treatment of High-Resolution Mass Spectrometry Data.

Complex molecular mixtures are encountered in almost all research disciplines, such as biomedical 'omics, petroleomics, and environmental sciences. State-of-the-art characterization of sample materials related to these fields, deploying high-end instrumentation, allows for gathering large quantities of molecular composition data. One established technological platform is ultrahigh-resolution mass spectrometry, e.g., Fourier-transform mass spectrometry (FT-MS). However, the huge amounts of data acquired in FT-MS often result in tedious data treatment and visualization. FT-MS analysis of complex matrices can easily lead to single mass spectra with more than 10,000 attributed unique molecular formulas. Sophisticated software solutions to conduct these treatment and visualization attempts from commercial and noncommercial origins exist. However, existing applications have distinct drawbacks, such as focusing on only one type of graphic representation, being unable to handle large data sets, or not being publicly available. In this respect, we developed a software, within the international complex matrices molecular characterization joint lab (IC2MC), named "python tools for complex matrices molecular characterization" (PyC2MC). This piece of software will be open-source and free to use. PyC2MC is written under python 3.9.7 and relies on well-known libraries such as pandas, NumPy, or SciPy. It is provided with a graphical user interface developed under PyQt5. The two options for execution, (1) a user-friendly route with a prepacked executable file or (2) running the main python script through a Python interpreter, ensure a high applicability but also an open characteristic for further development by the community. Both are available on the GitHub platform (https://github.com/iC2MC/PyC2MC_viewer).

Experimental study on the imidazoles of aqueous secondary organic aerosol formed from reaction of methylglyoxal and ammonium sulphate

Imidazole and its derivatives are the main heterocyclic nitrogen-containing brown carbon constituents in aerosol particles. Imidazoles of aqueous secondary organic aerosol (aqSOA) particles formed from the reaction of methylglyoxal and ammonium sulphate ((NH4)2SO4) are detected by vacuum ultraviolet photoionization aerosol mass spectrometer (VUV-PIMS) in real-time and verified off-line with optical spectrometry in current study. The experimental results showed that the single photon ionization mass spectrum of aqSOA particles measured by VUV-PIMS emerged the molecular ion peaks at m/z = 68, 82 and 110. While, the extraction solution of aqSOA particles detected by off-line techniques demonstrated that the characteristic peaks at 217 and 282 nm appeared in the UV–Vis spectrum; the strong emission in 405–480 nm with maximum emission wavelength at 435 nm contained in the 3D fluorescence spectra; and the chemical shift peaks of hydrogen atoms on N–H, CC and CN bond on imidazole ring and methyl group arised in the 1H-NMR spectrum. In view of these spectral information, 4-methyl-imidazole and 4-methyl-imidazole-2-carbaldehyde are determined as the principal products of the aqueous reaction between methylglyoxal and (NH4)2SO4. The possible reaction mechanism leading to the generation of imidazole compounds are also discussed. These will help to understand the formation process of imidazole compounds in atmospheric aerosol particles, and provide experimental basis for the model mechanism study of aqSOA particles.

Lipidomics of the Edible Brown Alga Wakame (Undaria pinnatifida) by Liquid Chromatography Coupled to Electrospray Ionization and Tandem Mass Spectrometry.

The lipidome of a brown seaweed commonly known as wakame (Undaria pinnatifida), which is grown and consumed around the world, including Western countries, as a healthy nutraceutical food or supplement, was here extensively examined. The study was focused on the characterization of phospholipids (PL) and glycolipids (GL) by liquid chromatography (LC), either hydrophilic interaction LC (HILIC) or reversed-phase LC (RPLC), coupled to electrospray ionization (ESI) and mass spectrometry (MS), operated both in high and in low-resolution mode. Through the acquisition of single (MS) and tandem (MS/MS) mass spectra more than 200 PL and GL of U. pinnatifida extracts were characterized in terms of lipid class, fatty acyl (FA) chain composition (length and number of unsaturations), and regiochemistry, namely 16 SQDG, 6 SQMG, 12 DGDG, 5 DGMG, 29 PG, 8 LPG, 19 PI, 14 PA, 19 PE, 8 PE, 38 PC, and 27 LPC. The FA (C16:0) was the most abundant saturated acyl chain, whereas the monounsaturated C18:1 and the polyunsaturated C18:2 and C20:4 chains were the prevailing ones. Odd-numbered acyl chains, iJ., C15:0, C17:0, C19:0, and C19:1, were also recognized. While SQDG exhibited the longest and most unsaturated acyl chains, C18:1, C18:2, and C18:3, in the sn-1 position of glycerol, they were preferentially located in the sn-2 position in the case of PL. The developed analytical approach might pave the way to extend lipidomic investigations also for other edible marine algae, thus emphasizing their potential role as a source of bioactive lipids.

Direct detection of OXA-48-like carbapenemase variants with and without co-expression of an extended-spectrum β-lactamase from bacterial cell lysates using mass spectrometry

IntroductionAntibiotic-resistant Gram-negative bacteria are of a growing concern globally, especially those producing enzymes conferring resistance. OXA-48-like carbapenemases hydrolyze most β-lactam antibiotics, with typically low-level hydrolysis of carbapenems, but have limited effect on broad-spectrum cephalosporins. These are frequently co-expressed with extended spectrum β-lactamases, especially CTX-M-15, which typically shows high level resistance to broad-spectrum cephalosporins, yet is carbapenem susceptible. The combined resistance profile makes the need for successful detection of these specific resistance determinants imperative for effective antibiotic therapy. ObjectivesThe objective of this study is to detect and identify OXA-48-like and CTX-M-15 enzymes using mass spectrometry, and to subsequently develop a method for detection of both enzyme types in combination with liquid chromatography. MethodsCells grown in either broth or on agar were harvested, lysed, and, in some cases buffer-exchanged. Lysates produced from bacterial cells were separated and analyzed via liquid chromatography with mass spectrometry (LC-MS) and tandem mass spectrometry (LC-MS/MS). ResultsThe intact proteins of OXA-48, OXA-181, and OXA-232 (collectively OXA-48-like herein) and CTX-M-15 were characterized and detected. Acceptance criteria based on sequence-informative fragments from each protein group were established as confirmatory markers for the presence of the protein(s). A total of 25 isolates were successfully tested for OXA-48 like (2), CTX-M-15 (3), or expression of both (7) enzymes. Thirteen isolates served as negative controls. ConclusionsHere we present a method for the direct and independent detection of both OXA-48-like carbapenemases and CTX-M-15 β-lactamases using LC-MS/MS. The added sensitivity of MS/MS allows for simultaneous detection of at least two co-eluting, co-isolated and co-fragmented proteins from a single mass spectrum.

ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry.

Top-down mass spectrometry (TD-MS) of peptides and proteins results in product ions that can be correlated to polypeptide sequence. Fragments can either be terminal fragments, which contain either the N- or the C-terminus, or internal fragments that contain neither termini. Normally, only terminal fragments are assigned due to the computational difficulties of assigning internal fragments. Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complementary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum. Data are available via the MassIVE community resource with the identifiers MSV000086788 and MSV000086789.

Decoding the protein composition of whole nucleosomes with Nuc-MS.

Current proteomics approaches disassemble and digest nucleosome particles, blurring the readout of the “histone code”. To preserve nucleosome-level information, we developed Nuc-MS which displays the landscape of histone variants and their PTMs in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (6-fold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (e.g., a >15-fold enrichment of H3K79me2). Nuc-MS is highly concordant with ChIP-seq and offers a new readout of nucleosome-level biology.

Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow.

MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.

Comprehensive Structural Characterization of Lipids by Coupling Paternò-Büchi Reaction and Tandem Mass Spectrometry.

Since the invention of soft ionization methods, in particular electrospray ionization (ESI), mass spectrometry (MS) has become the method of choice for both qualitative and quantitative analysis of lipids from complex samples. A large number of lipids can be readily detected from a single mass spectrum free from molecular fragmentation that may complicate spectral interpretation. This has been the driving force for MS to play a predominant role in lipidomics. However, elucidation of the detailed lipid structures, especially the location of carbon-carbon double bond (C=C), remains challenging for MS-based lipid analysis workflows. Here we describe the coupling of photochemical derivatization of C=C via Paternò-Büchi (PB) reaction with tandem mass spectrometry (MS/MS) to identify C=C locations in unsaturated lipids and quantify lipid C=C location isomers. The PB reaction can be conducted online in ~30s, which transforms a C=C into the oxetane ring structure. Subjecting PB products of lipids to MS/MS leads to the formation of abundant C=C-specific fragment ions upon low energy collision-induced dissociation.

Adduct annotation in liquid chromatography/high-resolution mass spectrometry to enhance compound identification

Annotation and interpretation of full scan electrospray mass spectra of metabolites is complicated by the presence of a wide variety of ions. Not only protonated, deprotonated, and neutral loss ions but also sodium, potassium, and ammonium adducts as well as oligomers are frequently observed. This diversity challenges automatic annotation and is often poorly addressed by current annotation tools. In many cases, annotation is integrated in metabolomics workflows and is based on specific chromatographic peak-picking tools. We introduce mzAdan, a nonchromatography-based multipurpose standalone application that was developed for the annotation and exploration of convolved high-resolution ESI-MS spectra. The tool annotates single or multiple accurate mass spectra using a customizable adduct annotation list and outputs a list of [M+H]+ candidates. MzAdan was first tested with a collection of 408 analytes acquired with flow injection analysis. This resulted in 402 correct [M+H]+ identifications and, with combinations of sodium, ammonium, and potassium adducts and water and ammonia losses within a tolerance of 10 mmu, explained close to 50% of the total ion current. False positives were monitored with mass accuracy and bias as well as chromatographic behavior which led to the identification of adducts with calcium instead of the expected potassium. MzAdan was then integrated in a workflow with XCMS for the untargeted LC-MS data analysis of a 52 metabolite standard mix and a human urine sample. The results were benchmarked against three other annotation tools, CAMERA, findMAIN, and CliqueMS: findMAIN and mzAdan consistently produced higher numbers of [M+H]+ candidates compared with CliqueMS and CAMERA, especially with co-eluting metabolites. Detection of low-intensity ions and correct grouping were found to be essential for annotation performance.Graphical abstract

Ultrahigh-Resolution Mass Spectrometry-Based Platform for Plasma Metabolomics Applied to Type 2 Diabetes Research.

Metabolomics-the endpoint of the omics cascade-is increasingly recognized as a preferred method for understanding the ultimate responses of biological systems to stress. Flow injection electrospray (FIE) mass spectrometry (MS) has advantages for untargeted metabolic fingerprinting due to its simplicity and capability for high-throughput screening but requires a high-resolution mass spectrometer to resolve metabolite features. In this study, we developed and validated a high-throughput and highly reproducible metabolomics platform integrating FIE with ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS for analysis of both polar and nonpolar metabolite features from plasma samples. FIE-FTICR MS enables high-throughput detection of hundreds of metabolite features in a single mass spectrum without a front-end separation step. Using plasma samples from genetically identical obese mice with or without type 2 diabetes (T2D), we validated the intra and intersample reproducibility of our method and its robustness for simultaneously detecting alterations in both polar and nonpolar metabolite features. Only 5 min is needed to acquire an ultra-high resolution mass spectrum in either a positive or negative ionization mode. Approximately 1000 metabolic features were reproducibly detected and annotated in each mouse plasma group. For significantly altered and highly abundant metabolite features, targeted tandem MS (MS/MS) analyses can be applied to confirm their identity. With this integrated platform, we successfully detected over 300 statistically significant metabolic features in T2D mouse plasma as compared to controls and identified new T2D biomarker candidates. This FIE-FTICR MS-based method is of high throughput and highly reproducible with great promise for metabolomics studies toward a better understanding and diagnosis of human diseases.

Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry.

Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation and electron transfer dissociation are widely used for these types of analyses. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons (>20 eV) has been suggested to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. Here, we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that include neither the C-terminus nor the N-terminus of the protein. Conventionally, internal fragments have been disregarded, as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ∼20-40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ∼50 to ∼99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. When searching for internal fragments during data analysis, previously unassigned peaks can be readily and accurately assigned to confirm a given protein sequence and to enhance the utility of top-down protein sequencing experiments.

KairosMS: A New Solution for the Processing of Hyphenated Ultrahigh Resolution Mass Spectrometry Data.

The use of hyphenated Fourier transform mass spectrometry (FTMS) methods affords additional information about complex chemical mixtures. Coeluted components can be resolved thanks to the ultrahigh resolving power, which also allows extracted ion chromatograms (EICs) to be used for the observation of isomers. As such data sets can be large and data analyses laborious, improved tools are needed for data analyses and extraction of key information. The typical workflow for this type of data is based upon manually dividing the total ion chromatogram (TIC) into several windows of usually equal retention time, averaging the signal of each window to create a single mass spectrum, extracting a peak list, performing the compositional assignments, visualizing the results, and repeating the process for each window. Through removal of the need to manually divide a data set into many time windows and analyze each one, a time-consuming workflow has been significantly simplified. An environmental sample from the oil sands region of Alberta, Canada, and dissolved organic matter samples from the Suwannee River Fulvic Acid (SRFA) and marine waters (Marine DOM) were used as a test bed for the new method. A complete solution named KairosMS was developed in the R language utilizing the Tidyverse packages and Shiny for the user interface. KairosMS imports raw data from common file types, processes it, and exports a mass list for compositional assignments. KairosMS then incorporates those assignments for analysis and visualization. The present method increases the computational speed while reducing the manual work of the analysis when compared to other current methods. The algorithm subsequently incorporates the assignments into the processed data set, generating a series of interactive plots, EICs for individual components or entire compound classes, and can export raw data or graphics for off-line use. Using the example of petroleum related data, it is then visualized according to heteroatom class, carbon number, double bond equivalents, and retention time. The algorithm also gives the ability to screen for isomeric contributions and to follow homologous series or compound classes, instead of individual components, as a function of time.

Chiral Discrimination by a Binuclear Pd Complex Sensor Using 31P{1H} NMR.

An axially chiral binuclear μ-hydroxo Pd complex (BPHP) first served as an excellent chiral sensor for discriminating a variety of analytes including amino alcohol, amino amide, amino acid, mandelic acid, diol, diamine, and monoamine by 31P{1H} NMR. A detailed recognition mechanism was proposed based on the single crystal and mass spectrum of Pd-complexes. In general, BPHP sensor, through extracting the acidic hydrogen of an analyte by its Pd-OH group, forms stable diastereomeric complexes with two enantiomers of the analyte giving well distinguishable split 31P{1H} NMR signals for chiral discrimination.

A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

Mass spectrometry (MS) based top-down proteomics provides rich information about proteoforms arising from combinatorial amino acid sequence variations and post-translational modifications (PTMs). Fourier transform ion cyclotron resonance (FT-ICR) MS affords ultrahigh resolving power and provides high-accuracy mass measurements, presenting a powerful tool for top-down MS characterization of proteoforms. However, the detection and characterization of large proteins from complex mixtures remain challenging due to the exponential decrease in S: N with increasing molecular weight (MW) and coeluting low-MW proteins; thus, size-based fractionation of complex protein mixtures prior to MS analysis is necessary. Here, we directly combine MS-compatible serial size exclusion chromatography (sSEC) fractionation with 12 T FT-ICR MS for targeted top-down characterization of proteins from complex mixtures extracted from human and swine heart tissue. Benefiting from the ultrahigh resolving power of FT-ICR, we isotopically resolved 31 distinct proteoforms (30-50 kDa) simultaneously in a single mass spectrum within a 100 m/ z window. Notably, within a 5 m/ z window, we obtained baseline isotopic resolution for 6 distinct large proteoforms (30-50 kDa). The ultrahigh resolving power of FT-ICR MS combined with sSEC fractionation enabled targeted top-down analysis of large proteoforms (>30 kDa) from the human heart proteome without extensive chromatographic separation or protein purification. Further separation of proteoforms inside the mass spectrometer (in-MS) allowed for isolation of individual proteoforms and targeted electron capture dissociation (ECD), yielding high sequence coverage. sSEC/FT-ICR ECD facilitated the identification and sequence characterization of important metabolic enzymes. This platform, which facilitates deep interrogation of proteoform primary structure, is highly tunable, allows for adjustment of MS and MS/MS parameters in real time, and can be utilized for a variety of complex protein mixtures.

Source apportionment using receptor model based on aerosol mass spectra and 1 h resolution chemical dataset in Tianjin, China

Source apportionment studies have been performed on online receptor datasets in recent years (called online source apportionment), including mass spectra and online chemical dataset. Single particle aerosol mass spectrometry (SPAMS), an important online technique, has the ability to analyze mass spectrum (MS) and particular size information of a single particle in real time. Clustering methods have been widely applied to MS dataset to investigate the sources of particles, although the receptor models are the common tools to probe the particle sources based on the receptor dataset. This work developed a new method (SPAMS-RM) that employed the receptor model (RM) on an MS dataset from SPAMS to identify particle sources. Particles were measured by SPAMS from July 14 to August 15, 2015, at an urban site in Tianjin, China. Multilinear Engine-2 (ME2) and adaptive resonance theory-based neural networks-2a (ART-2a) were separately used to analyze the single particle MS dataset. This work also evaluated the performance of SPAMS-RM method. Concentrations of chemical components of PM2.5 (particulate matter with an aerodynamic diameter of less than 2.5 μm) and gaseous pollutants were measured by independent online instruments (1 h resolution). Source apportionment was separately conducted using two receptor models, Positive Matrix Factorization (PMF) and ME2, based on the 1 h resolution chemical dataset. This method was called online chemical source apportionment (OCSA-RM). ART-2a obtained 19 clusters that merged into five major classes: carbon species, rich-K, sea salt, crustal dust, and industrial metals. SPAMS-RM identified eight sources by interpreting the MS characteristic of factors and investigating the relationship of the temporal trends of factor contributions, chemical species, gaseous pollutants, and particle clusters. OCSA-ME2 and OCSA-PMF both identified seven factors. Source apportionment results between SPAMS-RM and OCSA-ME2/PMF were compared. Each method identified coal combustion, biomass burning, sea salt, nitrate source, sulfate source, vehicle emission, and crustal dust. The SPAMS-RM results showed that nitrate source was the most significant contributor (34%) to the PM followed by sulfate source (17%), coal combustion (14%), crustal dust (11%), vehicle emission (10%), biomass burning-OCEC (7%), and industrial activities & sea salt (4%). Some differences between SPAMS-RM and OCSA-ME2/PMF results existed and might be due to chemical analysis methods and sampling methods. ME2 was used for the first time to identify the PM sources based on the MS dataset from SPAMS and demonstrated its capability when coupled with MS dataset from SPAMS to apportion the source of PM.

Simultaneous Detection of Vanadyl, Nickel, Iron, and Gallium Porphyrins in Marine Shales from the Eagle Ford Formation, South Texas

Metalloporphyrins in immature shales of the Late Cretaceous Eagle Ford Formation from South Texas were analyzed by positive-ion electrospray ionization (ESI) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Vanadyl, nickel, iron, and gallium porphyrins were detected in a single mass spectrum. The iron porphyrins were most abundant, followed by vanadyl, nickel, and gallium porphyrins, consistent with the metal contents determined by elemental analysis. The distribution of porphyrins shows that deoxophylloerythroetio (DPEP) porphyrins, dicyclic-deoxophylloerythroetio (di-DPEP) porphyrins, and porphyrins containing oxygen functional groups are the main components. The detection of oxygen-containing porphyrins, such as iron porphyrins with formulas of CnHmN4FeO, CnHmN4FeO2, and CnHmN5FeO2, would offer new clues of petroporphyrins formation mechanism from biological sources, such as chlorophylls and hemes. To our knowledge, this reports for the first time the presence of oxygen-containing iron porphyrins and gallium porphyrins in geological samples other than coals and lignites. The discovery of these petroporphyrins could provide additional insights into the diagenetic pathway of petroporphyrins and novel applications in petroleum geochemistry/exploration and oil refining. The composition of metalloporphyrins may potentially provide clues to decipher the redox conditions during deposition in the Eagle Ford Formation and provide better understanding of the Oceanic Anoxic Event 2 (OAE-2).

Micro-Data-Independent Acquisition for High-Throughput Proteomics and Sensitive Peptide Mass Spectrum Identification.

State-of-the-art strategies for proteomics are not able to rapidly interrogate complex peptide mixtures in an untargeted manner with sensitive peptide and protein identification rates. We describe a data-independent acquisition (DIA) approach, microDIA (μDIA), that applies a novel tandem mass spectrometry (MS/MS) mass spectral deconvolution method to increase the specificity of tandem mass spectra acquired during proteomics experiments. Using the μDIA approach with a 10 min liquid chromatography gradient allowed detection of 3.1-fold more HeLa proteins than the results obtained from data-dependent acquisition (DDA) of the same samples. Additionally, we found the μDIA MS/MS deconvolution procedure is critical for resolving modified peptides with relatively small precursor mass shifts that cause the same peptide sequence in modified and unmodified forms to theoretically cofragment in the same raw MS/MS spectra. The μDIA workflow is implemented in the PROTALIZER software tool which fully automates tandem mass spectral deconvolution, queries every peptide with a library-free search algorithm against a user-defined protein database, and confidently identifies multiple peptides in a single tandem mass spectrum. We also benchmarked μDIA against DDA using a 90 min gradient analysis of HeLa and Escherichia coli peptides that were mixed in predefined quantitative ratios, and our results showed μDIA provided 24% more true positives at the same false positive rate.

Chiral and molecular recognition of monosaccharides by photoexcited tryptophan in cold gas-phase noncovalent complexes as a model for chemical evolution in interstellar molecular clouds.

Chiral and molecular recognition between amino acid and sugar molecules and their implications for chemical evolution were investigated using a tandem mass spectrometer equipped with an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation of mass-selected and temperature-controlled gas-phase noncovalent complexes of protonated tryptophan (Trp) and monosaccharide enantiomers, such as aldohexose, aldopentose, and deoxyhexose, was examined as a model for chemical evolution in interstellar molecular clouds. Upon photoexcitation of noncovalent heterochiral H+(L-Trp)(D-aldohexose) complexes, NH2CHCOOH loss from protonated Trp via Cα-Cβ bond cleavage occurred. Conversely, in homochiral H+(L-Trp)(L-aldohexose), the energy absorbed by Trp was released through the detachment of aldohexose, and dissociation of the amino acid was suppressed. In the photodissociation mass spectra of protonated Trp with aldopentose and deoxyhexose, which lacks the OH group of aldohexose, no dissociation of the molecules in the complexes or differences between enantiomers were observed. These results indicate that the OH groups in monosaccharides contribute to enantiomer-selective photodissociation in molecular clouds. The differences observed between enantiomers in the photodissociation mass spectra were applied to distinguishing and quantifying aldohexose enantiomers in solution using L-Trp as a chiral probe. The enantiomeric excesses of aldohexoses in solution could be determined from a single photodissociation mass spectrum by reference to the relative ion intensities for the NH2CHCOOH-elimination product and H+(L-Trp) formed via detachment of aldohexose. This analysis method could also distinguish and quantify two D-aldohexose mixtures, where L-Trp was employed as an isomer probe. Graphical abstract ᅟ.

A combined photoionization time-of-flight mass spectrometry and laser absorption spectrometry flash photolysis apparatus for simultaneous determination of reaction rates and product branching.

In recent years, predictions of product branching for reactions of consequence to both combustion and atmospheric chemistry have outpaced validating experiments. An apparatus is described that aims to fill this void by combining several well-known experimental techniques into one: flash photolysis for radical generation, multiple-pass laser absorption spectrometry (LAS) for overall kinetics measurements, and time-resolved photoionization time-of-flight mass spectrometry (PI TOF-MS) for product branching quantification. The sensitivity of both the LAS and PI TOF-MS detection techniques is shown to be suitable for experiments with initial photolytically generated radical concentrations of ∼1 × 1012 molecules cm-3. As it is fast (μs time resolution) and non-intrusive, LAS is preferred for accurate kinetics (time-dependence) measurements. By contrast, PI TOF-MS is preferred for product quantification because it provides a near-complete picture of the reactor composition in a single mass spectrum. The value of simultaneous LAS and PI TOF-MS detection is demonstrated for the chemically interesting phenyl radical + propene system.