Tandem Spectra Research Articles

Jupiter and Saturn as Spectral Analogs for Extrasolar Gas Giants and Brown Dwarfs

With the advent of direct-imaging spectroscopy, the number of spectra from brown dwarfs and extrasolar gas giants is growing rapidly. Many brown dwarfs and extrasolar gas giants exhibit spectroscopic and photometric variability, which is likely the result of weather patterns. However, for the foreseeable future, point-source observations will be the only viable method to extract brown dwarf and exoplanet spectra. Models have been able to reproduce the observed variability, but ground-truth observations are required to verify their results. To that end, we provide visual and near-infrared spectra of Jupiter and Saturn obtained from the Cassini VIMS instrument. We disk-integrate the VIMS spectral cubes to simulate the spectra of Jupiter and Saturn as if they were directly imaged exoplanets or brown dwarfs. We present six empirical disk-integrated spectra for both Jupiter and Saturn with phase coverage of 1.°7–133.°5 and 39.°6–110.°2, respectively. To understand the constituents of these disk-integrated spectra, we also provide end-member (single-feature) spectra for permutations of illumination and cloud density, as well as for Saturn’s rings. In tandem, these disk-integrated and end-member spectra provide the ground truth needed to analyze point-source spectra from extrasolar gas giants and brown dwarfs. Lastly, we discuss the impact that icy rings, such as Saturn’s, have on disk-integrated spectra and consider the feasibility of inferring the presence of rings from direct-imaging spectra.

Mass Spectral Library Methods for Analysis of Site-Specific N-Glycosylation: Application to Human Milk Proteins.

We present a mass spectral library-based method for analyzing site-specific N-linked protein glycosylation. Its operation and utility are illustrated by applying it to both newly measured and available proteomics data of human milk glycoproteins. It generates two varieties of mass spectral libraries. One contains glycopeptide abundance distribution spectra (GADS). The other contains tandem mass spectra of the underlying glycopeptides. Both originate from identified glycopeptides in proteolytic digests of human milk and purified glycoproteins, which include tenascin, lactoferrin, and several antibodies. Analysis was also applied to digests of a NIST human milk standard reference material (SRM), leading to a GADS library of N-glycopeptides, enabling the direct comparison of glycopeptide distributions for individual proteins. Tandem spectra underlying each glycopeptide GADS peak are combined to create a second type of library that contains spectra of the underlying glycopeptide spectra. These were acquired by higher-energy (stepped) collision dissociation fragmentation followed by ion-trap fragmentation. Spectra are annotated using MS_Piano, recently reported annotation software. This data, with extensions of a widely used spectral library search and display software, provides accessible mass spectral libraries.

DDA-imaging with structural identification of lipid molecules on an Orbitrap Velos Pro mass spectrometer.

Matrix‐assisted laser desorption/ionization‐mass spectrometry imaging (MALDI‐MSI) is a useful technique for visualizing the spatial distribution of lipid molecules in tissues. Nevertheless, the use of MSI to investigate local lipid metabolic hallmarks has until recently been hampered by a lack of adequate technology that supports confident lipid identification. This limitation was recently mitigated by the development of DDA‐imaging technology where high‐resolution MSI is combined with parallel acquisition of lipid tandem MS2 spectra on a hybrid ion trap‐Orbitrap Elite mass spectrometer featuring a resolving power of 240,000 and a scan time of 1 s. Here, we report the key tenets related to successful transfer of the DDA‐imaging technology onto an Orbitrap Velos Pro instrument featuring a resolving power of 120,000 and a scan time of 2 s. Through meticulous performance assessments and method optimization, we tuned the DDA‐imaging method to be able to confidently identify 73 molecular lipid species in mouse brain sections and demonstrate that the performance of the technology is comparable with DDA‐imaging on the Orbitrap Elite. Altogether, our work shows that DDA‐imaging on the Orbitrap Velos Pro instrument can serve as a robust workhorse for lipid imaging in routine applications.

How Well Can We Predict Mass Spectra from Structures? Benchmarking Competitive Fragmentation Modeling for Metabolite Identification on Untrained Tandem Mass Spectra.

Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID) is a machine learning tool to predict in silico tandem mass spectra (MS/MS) for known or suspected metabolites for which chemical reference standards are not available. As a machine learning tool, it relies on both an underlying statistical model and an explicit training set that encompasses experimental mass spectra for specific compounds. Such mass spectra depend on specific parameters such as collision energies, instrument types, and adducts which are accumulated in libraries. Yet, ultimately prediction tools that are meant to cover wide expanses of entities must be validated on cases that were not included in the initial training and testing sets. Hence, we here benchmarked the performance of CFM-ID 4.0 to correctly predict MS/MS spectra for spectra that were not included in the CFM-ID training set and for different mass spectrometry conditions. We used 609,456 experimental tandem spectra from the NIST20 mass spectral library that were newly added to the previous NIST17 library version. We found that CFM-ID's highest energy prediction output would maximize the capacity for library generation. Matching the experimental collision energy with CFM-ID's prediction energy produced the best results, even for HCD-Orbitrap instruments. For benzenoids, better MS/MS predictions were achieved than for heterocyclic compounds. However, when exploring CFM-ID's performance on 8,305 compounds at 40 eV HCD-Orbitrap collision energy, >90% of the 20/80 split test compounds showed <700 MS/MS similarity score. Instead of a stand-alone tool, CFM-ID 4.0 might be useful to boost candidate structures in the greater context of identification workflows.

Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification.

Mass spectrometric profiling provides information on the protein and metabolic composition of biological samples. However, the weak efficiency of computational algorithms in correlating tandem spectra to molecular components (proteins and metabolites) dramatically limits the use of “omics” profiling for the classification of nosologies. The development of machine learning methods for the intelligent analysis of raw mass spectrometric (HPLC-MS/MS) measurements without involving the stages of preprocessing and data identification seems promising. In our study, we tested the application of neural networks of two types, a 1D residual convolutional neural network (CNN) and a 3D CNN, for the classification of three cancers by analyzing metabolomic-proteomic HPLC-MS/MS data. In this work, we showed that both neural networks could classify the phenotypes of gender-mixed oncology, kidney cancer, gender-specific oncology, ovarian cancer, and the phenotype of a healthy person by analyzing ‘omics’ data in ‘mgf’ data format. The created models effectively recognized oncopathologies with a model accuracy of 0.95. Information was obtained on the remoteness of the studied phenotypes. The closest in the experiment were ovarian cancer, kidney cancer, and prostate cancer/kidney cancer. In contrast, the healthy phenotype was the most distant from cancer phenotypes and ovarian and prostate cancers. The neural network makes it possible to not only classify the studied phenotypes, but also to determine their similarity (distance matrix), thus overcoming algorithmic barriers in identifying HPLC-MS/MS spectra. Neural networks are versatile and can be applied to standard experimental data formats obtained using different analytical platforms.

Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation.

Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP+ and TMPP-Ac-NH2/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.

Tandem surface-induced dissociation of protein complexes on an ultrahigh resolution platform

We describe instrumentation for conducting tandem surface-induced dissociation (tSID) of native protein complexes on an ultrahigh resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The two stages of SID are accomplished with split lenses replacing the entrance lenses of the quadrupole mass filter (stage 1, referred to herein as SID-Q) and the collision cell (stage 2, Q-SID). After SID-Q, the scattered projectile ions and subcomplexes formed in transit traverse the pre-filter prior to the mass-selecting quadrupole, providing preliminary insights into the SID fragmentation kinetics of noncovalent protein complexes. The isolated SID fragments (subcomplexes) are then fragmented by SID in the collision cell entrance lens (Q-SID), generating subcomplexes of subcomplexes. We show that the ultrahigh resolution of the FT-ICR can be used for deconvolving species overlapping in m/z, which are particularly prominent in tandem SID spectra due to the combination of symmetric charge partitioning and narrow product ion charge state distributions. Various protein complex topologies are explored, including homotetramers, homopentamers, a homohexamer, and a heterohexamer.

Mass Spectral Library of Acylcarnitines Derived from Human Urine.

We describe the creation of a mass spectral library of acylcarnitines and conjugated acylcarnitines from the LC-MS/MS analysis of six NIST urine reference materials. To recognize acylcarnitines, we conducted in-depth analyses of fragmentation patterns of acylcarnitines and developed a set of rules, derived from spectra in the NIST17 Tandem MS Library and those identified in urine, using the newly developed hybrid search method. Acylcarnitine tandem spectra were annotated with fragments from carnitine and acyl moieties as well as neutral loss peaks from precursors. Consensus spectra were derived from spectra having similar retention time, fragmentation pattern, and the same precursor m/z and collision energy. The library contains 157 different precursor masses, 586 unique acylcarnitines, and 4 332 acylcarnitine consensus spectra. Furthermore, from spectra that partially satisfied the fragmentation rules of acylcarnitines, we identified 125 conjugated acylcarnitines represented by 987 consensus spectra, which appear to originate from Phase II biotransformation reactions. To our knowledge, this is the first report of conjugated acylcarnitines. The mass spectra provided by this work may be useful for clinical screening of acylcarnitines as well as for studying relationships among fragmentation patterns, collision energies, structures, and retention times of acylcarnitines. Further, these methods are extensible to other classes of metabolites.

Glycan reductive amino acid coded affinity tagging (GRACAT) for highly specific analysis of N-glycome by mass spectrometry

N-glycans are involved in a variety of biological processes and associated with many diseases. However, the sensitive and specific detection of glycans via mass spectrometry (MS) remains challenging due to their relatively low abundance and low ionization efficiency. In this work, a new method termed glycan reductive amino acid coded affinity tagging (GRACAT) is developed to address these problems. Through labeling the reducing ends of glycan with a biotinylated arginine, the ionization efficiency of glycan was increased nearly 50-fold and glycan isomers were discriminated by improved signals of fragments in tandem spectra. Moreover, the strong affinity interaction between streptavidin and biotin enabled highly specific enrichment of the biotin-tagged glycans from the mixture of proteins and peptides. We successfully applied GRACAT in the profiling of N-glycome in human serum and bovine milk, in which a total of 55 and 67 N-glycans were detected respectively.

Meet the Associate Editors: Tara Pukala

Meet the Associate Editors: Tara Pukala

Anthocyanidins structural study using positive electrospray ionization triple quadrupole mass spectrometry and H/D exchange.

We report herein a detailed structural study by collision-induced dissociation (CID) of nonglycosylated anthocyanins (anthocyanidins) using electrospray ionization triple quadrupole mass spectrometry (ESI-QqQ) and isotope labeling experiments to understand the fragmentation process often used in mass spectrometry analysis of this class of compounds. Tandem mass spectrometric product ion spectra for three anthocyanidins (cyanidin, delphynidin, and pelargonin) were evaluated to propose fragmentation mechanisms to this natural colorant class of organic compounds. The proposed rearrangements, retro Diels-Alder reaction, water loss, CO losses, and stable acylium ion formation, were evaluated based on tandem mass spectrometric experiments of normal and labeled precursor ions together to computational thermochemistry. B3LYP/6-311+G** ab initio calculations studies were carried out to obtain energy diagrams to show the viability of the proposed mechanisms. The CO losses fragmentation channels have lower energies when compared with water losses and the other proposed fragmentations. The isotope labeling experiments indicate the H/D exchange of the hydroxyl protons and corroborate the proposed general fragmentation mechanism for anthocyanidins.

Synthesis, Characterization, and Thermal Decomposition of a New Energetic Salt 3-Amino-1,2,4-Triazole Dinitramide

ABSTRACTA new energetic salt, 3-amino-1,2,4-triazole dinitramide (ATADN), was synthesized through the combination of 3-amino-1,2,4-triazole cation and oxygen-rich dinitramide anion. The structure of ATADN was confirmed by single-crystal X-ray diffraction, elemental analysis, Fourier transform infrared spectroscopy, ultraviolet–visible spectrometry, and nuclear magnetic resonance spectroscopy. The thermal stability of ATADN was studied using differential scanning calorimetry, thermogravimetric analysis (TG), and TG tandem infrared spectrum. The thermal decomposition kinetics parameter was also calculated using the differential thermal analysis data based on Kissinger’s method. Results indicated that ATADN exhibited resistance to thermal decompositions of up to 439 K, and a corresponding activation energy of Ea = 281.9 kJ·mol−1. Moreover, its mechanical sensitivity and detonation properties were evaluated, which showed promising results for its potential application as a highly explosive compound.

ToF-SIMS Parallel Imaging MS/MS of Lipid Species in Thin Tissue Sections.

Unambiguous identification of detected species is essential in complex biomedical samples. To date, there are not many mass spectrometry imaging techniques that can provide both high spatial resolution and identification capabilities. A new and patented imaging tandem mass spectrometer, exploiting the unique characteristics of the nanoTOF II (Physical Electronics, USA) TOF-SIMS TRIFT instrument, was developed to address this.Tandem mass spectrometry is based on the selection of precursor ions from the full secondary ion spectrum (MS1), followed by energetic activation and fragmentation, and collection of the fragment ions to obtain a tandem MS spectrum (MS2). The PHI NanoTOF II mass spectrometer is equipped with a high-energy collision induced dissociation (CID) fragmentation cell as well as a second time-of-flight analyzer developed for simultaneous ToF-SIMS and tandem MS imaging experiments.We describe here the results of a ToF-SIMS imaging experiment on a thin tissue section of an infected zebrafish as a model organism for tuberculosis. The focus is on the obtained ion distribution plot of a fatty acid as well as its identification by tandem mass spectrometry.

Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides.

Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragmented glycans. Here, we investigated the link between glycan structures and the intensity of oxonium ions in the spectra of glycopeptides and utilized this information to improve the identification of glycopeptides in biological samples. Tandem spectra of glycopeptides from fetuin, glycophorin A, ovalbumin and gp120 tryptic digests were used to build a spectral database of N- and O-linked glycopeptides. Logistic regression was applied to this database to develop model to distinguish between the spectra of N- and O-linked glycopeptides. Remarkably, the developed model was found to reliably distinguish between the N- and O-linked glycopeptides using the spectral features of the oxonium ions using verification spectral set. Finally, the performance of the developed predictive model was evaluated in HILIC enriched glycopeptides extracted from human serum. The results showed that pre-classification of tandem spectra based on their glycosylation type improved the identification of N-linked glycopeptides. The developed model facilitates interpretation of tandem mass spectrometry data for assignment of glycopeptides.

Novel members of the adipokinetic hormone family in beetles of the superfamily Scarabaeoidea

Eight beetle species of the superfamily Scarabaeoidea were investigated with respect to peptides belonging to the adipokinetic hormone (AKH) family in their neurohemal organs, the corpora cardiaca (CC). The following beetle families are represented: Scarabaeidae, Lucanidae, and Geotrupidae. AKH peptides were identified through a heterospecific trehalose-mobilizing bioassay and by sequence analyses, using liquid chromatography coupled to positive electrospray mass spectrometry (LC-ESI-MS) and analysis of the tandem MS2 spectra obtained by collision-induced dissociation. All the beetle species have octapeptide AKHs; some have two AKHs, while others have only one. Novel AKH members were found in Euoniticellus intermedius and Circellium bacchus (family Scarabaeidae), as well as in Dorcus parallelipipedus (family Lucanidae). Two species of the family Geotrupidae and two species of the Scarabaeidae subfamily Cetoniinae contain one known AKH peptide, Melme-CC, while E. intermedius produces a novel peptide code named Euoin-AKH: pEINFTTGWamide. Two AKH peptides were each identified in CC of C. bacchus and D. parallelipipedus: the novel Cirba-AKH: pEFNFSAGWamide and the known peptide, Scade-CC-I in the former, and the novel Dorpa-AKH: pEVNYSPVW amide and the known peptide, Melme-CC in the latter. Kheper bonelli (subfamily Scarabaeinae) also has two AKHs, the known Scade-CC-I and Scade-CC-II. All the novel peptides were synthesized and the amino acid sequence assignments were unequivocally confirmed by co-elution of the synthetic peptides with their natural equivalent, and identical MS parameters of the two forms. The novel synthetic peptides are all active in inducing hypertrehalosemia in cockroaches.

Synthesis, Characterization, Thermal Stability and Sensitivity Properties of New Energetic Polymers-PVTNP-g-GAPs Crosslinked Polymers.

A series of energetic polymers, poly(vinyl 2,4,6-trinitrophenylacetal)-g-polyglycidylazides (PVTNP-g-GAPs), were synthesized via cross-linking reactions of PVTNP with three different molecular weight GAPs using toluene diisocyanate as the cross-linking agent. The structures of these energetic polymers were characterized by ultraviolet visible spectra (UV–Vis), attenuated total reflectance-Fourier transform-infrared spectroscopy (ATR-FTIR), and nuclear magnetic resonance spectrometry (NMR). The glass-transition temperatures of these energetic polymers were measured with differential scanning calorimetry (DSC) method, and the results showed that all the measured energetic polymers have two distinct glass-transition temperatures. The thermal decomposition behaviors of these energetic polymers were evaluated by differential thermal analysis (DTA), thermogravimetric analysis (TGA) and thermogravimetric analysis tandem infrared spectrum (TGA-IR). The results indicated that all the measured energetic polymers have excellent resistance to thermal decomposition up to 200 °C, and the initial thermal decomposition was attributed to the breakdown of azide group. Moreover, the sensitivity properties of these energetic polymers were measured with the national military standard methods and their compatibilities with the main energetic components of 2,4,6-trinitrotoluene (TNT)-based melt-cast explosive were evaluated by using the DTA method. The results indicate that these energetic polymers have feasible mechanical sensitivities and can be safely used with TNT, cyclotetramethylene tetranitramine (HMX), 1,1-diamino-2,2-dinitroethene (FOX-7), 3-nitro-1,2,4-triazol-5-one (NTO) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB).

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry

Based on conventional data-dependent acquisition strategy of shotgun proteomics, we present a new workflow DeMix, which significantly increases the efficiency of peptide identification for in-depth shotgun analysis of complex proteomes. Capitalizing on the high resolution and mass accuracy of Orbitrap-based tandem mass spectrometry, we developed a simple deconvolution method of “cloning” chimeric tandem spectra for cofragmented peptides. Additional to a database search, a simple rescoring scheme utilizes mass accuracy and converts the unwanted cofragmenting events into a surprising advantage of multiplexing. With the combination of cloning and rescoring, we obtained on average nine peptide-spectrum matches per second on a Q-Exactive workbench, whereas the actual MS/MS acquisition rate was close to seven spectra per second. This efficiency boost to 1.24 identified peptides per MS/MS spectrum enabled analysis of over 5000 human proteins in single-dimensional LC-MS/MS shotgun experiments with an only two-hour gradient. These findings suggest a change in the dominant “one MS/MS spectrum - one peptide” paradigm for data acquisition and analysis in shotgun data-dependent proteomics. DeMix also demonstrated higher robustness than conventional approaches in terms of lower variation among the results of consecutive LC-MS/MS runs.

Tandem Mass Spectral Libraries of Peptides in Digests of Individual Proteins: Human Serum Albumin (HSA)

This work presents a method for creating a mass spectral library containing tandem spectra of identifiable peptide ions in the tryptic digestion of a single protein. Human serum albumin (HSA(1)) was selected for this purpose owing to its ubiquity, high level of characterization and availability of digest data. The underlying experimental data consisted of ∼3000 one-dimensional LC-ESI-MS/MS runs with ion-trap fragmentation. In order to generate a wide range of peptides, studies covered a broad set of instrument and digestion conditions using multiple sources of HSA and trypsin. Computer methods were developed to enable the reliable identification and reference spectrum extraction of all peptide ions identifiable by current sequence search methods. This process made use of both MS2 (tandem) spectra and MS1 (electrospray) data. Identified spectra were generated for 2918 different peptide ions, using a variety of manually-validated filters to ensure spectrum quality and identification reliability. The resulting library was composed of 10% conventional tryptic and 29% semitryptic peptide ions, along with 42% tryptic peptide ions with known or unknown modifications, which included both analytical artifacts and post-translational modifications (PTMs) present in the original HSA. The remaining 19% contained unexpected missed-cleavages or were under/over alkylated. The methods described can be extended to create equivalent spectral libraries for any target protein. Such libraries have a number of applications in addition to their known advantages of speed and sensitivity, including the ready re-identification of known PTMs, rejection of artifact spectra and a means of assessing sample and digestion quality.

Fast Top-Down Intact Protein Characterization with Capillary Zone Electrophoresis–Electrospray Ionization Tandem Mass Spectrometry

Capillary zone electrophoresis (CZE)-electrospray ionization tandem mass spectrometry (ESI-MS/MS) was applied for rapid top-down intact protein characterization. A mixture containing four model proteins (cytochrome c, myoglobin, bovine serum albumin (BSA), and β-casein) was used as the sample. The CZE-ESI-MS system was first evaluated with the mixture. The four model proteins and five impurities were baseline-separated within 12 min. The limits of detection [signal-to-noise ratio (S/N) = 3] of the four model proteins ranged from 20 (cytochrome c) to 800 amol (BSA). The relative standard deviations of migration time and intensity for the four model proteins were less than 3% and 30%, respectively, in quintuplicate runs. CZE-ESI-MS/MS was then applied for top-down characterization of the mixture. Three of the model proteins (all except BSA) and an impurity (bovine transthyretin) were confidently identified by database searching of the acquired tandem spectra from protein fragmentation. Modifications including phosphorylation, N-terminal acetylation, and heme group binding were identified.

PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta‐analysis

The analysis of peptides and proteins in complex biological systems has greatly improved over the last decade. State-of-the-art mass spectrometric instruments combined with adequate software tools allow for more and more comprehensive proteome analyses. Most proteome-wide studies focus on the analysis of unmodified proteins or look at selected modifications only. However, spectral information of protein modifications, chemically induced through sample preparation or post-translationally attached in biological pathways is acquired as a significant, yet disregarded, fraction of tandem spectra in most discovery studies. We present a new computational pipeline, PTMeta, to uncover information of modifications attached to peptides. We use modification prescanning to pinpoint the most abundant potential modifications, followed by extensive database search and a statistical framework to combine results from database search runs with different modification settings.