Complementary Mass Spectrometric Techniques Research Articles

Composition and Sources of Organic Aerosol in Two Megacities in Western China Using Complementary Mass Spectrometric and Statistical Techniques.

Over 300 daily PM2.5 filter samples were collected in two western Chinese megacities, Xi'an and Chongqing, from October 2019 to May 2020. Their aqueous extracts were nebulized simultaneously to an aerosol mass spectrometer (AMS) and a recently developed extractive electrospray ionization (EESI) mass spectrometer, for bulk and near-molecular organic aerosol (OA) composition, respectively. Carbonate was quantified using EESI and a total organic carbon analyzer to separate inorganic carbon from dust. Via isotopically-labelled internal standards and positive matrix factorization, seven water-soluble sources were quantified separately using the AMS- and EESI-based analyses, with consistent types, concentrations, and correlations. These include dust, solid fuel combustion (SFC)-related, nitrogen- (and sulfur-) containing, summer/winter oxygenated OAs, and a cigarette-related OA only in EESI. When accounting for water-solubility, SFC-related OAs were the largest (53%) sources in Chongqing, while dust (consisting of 77% OA and 23% carbonates) was the largest (30%) source in Xi'an. Overall, this study presents one of the first times that complementary mass spectrometric techniques independently resolved consistent OA sources-with added chemical information-over multiple seasons and locations of complex pollution. The methods and quantified sources are essential for subsequent chemical, modelling, and health studies, and policy making for air pollution mitigation.

MMP-14 degrades tropoelastin and elastin

Matrix metalloproteinases are a class of enzymes, which degrade extracellular matrix components such as collagens, elastin, laminin or fibronectin. So far, four matrix metalloproteinases have been shown to degrade elastin and its precursor tropoelastin, namely matrix metalloproteinase-2, -7, -9 and -12. This study focuses on investigating the elastinolytic capability of membrane-type 1 matrix metalloproteinase, also known as matrix metalloproteinase-14. We digested recombinant human tropoelastin and human skin elastin with matrix metalloproteinase-14 and analyzed the peptide mixtures using complementary mass spectrometric techniques and bioinformatics tools. The results and additional molecular docking studies show that matrix metalloproteinase-14 cleaves tropoelastin as well as elastin. While tropoelastin was well degraded, fewer cleavages occurred in the highly cross-linked mature elastin. The study also provides insights into the cleavage preferences of the enzyme. Similar to cleavage preferences of matrix metalloproteinases-2, -7, -9 and -12, matrix metalloproteinase-14 prefers small and medium-sized hydrophobic residues including Gly, Ala, Leu and Val at cleavage site P1’. Pro, Gly and Ala were preferably found at P1-P4 and P2′-P4′ in both tropoelastin and elastin. Cleavage of mature skin elastin by matrix metalloproteinase-14 released a variety of bioactive elastin peptides, which indicates that the enzyme may play a role in the development and progression of cardiovascular diseases that go along with elastin breakdown.

The strength in numbers: comprehensive characterization of house dust using complementary mass spectrometric techniques

Untargeted analysis of a composite house dust sample has been performed as part of a collaborative effort to evaluate the progress in the field of suspect and nontarget screening and build an extensive database of organic indoor environment contaminants. Twenty-one participants reported results that were curated by the organizers of the collaborative trial. In total, nearly 2350 compounds were identified (18%) or tentatively identified (25% at confidence level 2 and 58% at confidence level 3), making the collaborative trial a success. However, a relatively small share (37%) of all compounds were reported by more than one participant, which shows that there is plenty of room for improvement in the field of suspect and nontarget screening. An even a smaller share (5%) of the total number of compounds were detected using both liquid chromatography–mass spectrometry (LC-MS) and gas chromatography–mass spectrometry (GC-MS). Thus, the two MS techniques are highly complementary. Most of the compounds were detected using LC with electrospray ionization (ESI) MS and comprehensive 2D GC (GC×GC) with atmospheric pressure chemical ionization (APCI) and electron ionization (EI), respectively. Collectively, the three techniques accounted for more than 75% of the reported compounds. Glycols, pharmaceuticals, pesticides, and various biogenic compounds dominated among the compounds reported by LC-MS participants, while hydrocarbons, hydrocarbon derivatives, and chlorinated paraffins and chlorinated biphenyls were primarily reported by GC-MS participants. Plastics additives, flavor and fragrances, and personal care products were reported by both LC-MS and GC-MS participants. It was concluded that the use of multiple analytical techniques was required for a comprehensive characterization of house dust contaminants. Further, several recommendations are given for improved suspect and nontarget screening of house dust and other indoor environment samples, including the use of open-source data processing tools. One of the tools allowed provisional identification of almost 500 compounds that had not been reported by participants.

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is therefore fundamental for the understanding of cellular processes. However, many protein complexes are dynamic assemblies and are not accessible by conventional structural techniques. Mass spectrometry contributes to the structural investigation of these assemblies, and particularly the combination of various mass spectrometric techniques delivers valuable insights into their structural arrangement. In this article, we describe the application and combination of two complementary mass spectrometric techniques, namely chemical cross-linking coupled with mass spectrometry and native mass spectrometry. Chemical cross-linking involves the covalent linkage of amino acids in close proximity by using chemical reagents. After digestion with proteases, cross-linked di-peptides are identified by mass spectrometry and protein interactions sites are uncovered. Native mass spectrometry on the other hand is the analysis of intact protein assemblies in the gas phase of a mass spectrometer. It reveals protein stoichiometries as well as protein and ligand interactions. Both techniques therefore deliver complementary information on the structure of protein-ligand assemblies and their combination proved powerful in previous studies.

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies.

Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is therefore fundamental for the understanding of cellular processes. However, many protein complexes are dynamic assemblies and are not accessible by conventional structural techniques. Mass spectrometry contributes to the structural investigation of these assemblies, and particularly the combination of various mass spectrometric techniques delivers valuable insights into their structural arrangement.In this article, we describe the application and combination of two complementary mass spectrometric techniques, namely chemical cross-linking coupled with mass spectrometry and native mass spectrometry. Chemical cross-linking involves the covalent linkage of amino acids in close proximity by using chemical reagents. After digestion with proteases, cross-linked di-peptides are identified by mass spectrometry and protein interactions sites are uncovered. Native mass spectrometry on the other hand is the analysis of intact protein assemblies in the gas phase of a mass spectrometer. It reveals protein stoichiometries as well as protein and ligand interactions. Both techniques therefore deliver complementary information on the structure of protein-ligand assemblies and their combination proved powerful in previous studies.

Real-time detection of highly oxidized organosulfates and BSOA marker compounds during the F-BEACh 2014 field study

Abstract. The chemical composition of ambient organic aerosols was analyzed using complementary mass spectrometric techniques during a field study in central Europe in July 2014 (Fichtelgebirge – Biogenic Emission and Aerosol Chemistry, F-BEACh 2014). Among several common biogenic secondary organic aerosol (BSOA) marker compounds, 93 acidic oxygenated hydrocarbons were detected with elevated abundances and were thus attributed to be characteristic for the organic aerosol mass at the site. Monoterpene measurements exhibited median mixing ratios of 1.6 and 0.8 ppbV for in and above canopy levels respectively. Nonetheless, concentrations for early-generation oxidation products were rather low, e.g., pinic acid (c = 4.7 (±2.5) ng m−3). In contrast, high concentrations were found for later-generation photooxidation products such as 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA, c = 13.8 (±9.0) ng m−3) and 3-carboxyheptanedioic acid (c = 10.2 (±6.6) ng m−3), suggesting that aged aerosol masses were present during the campaign period. In agreement, HYSPLIT trajectory calculations indicate that most of the arriving air masses traveled long distances (> 1500 km) over land with high solar radiation. In addition, around 47 % of the detected compounds from filter sample analysis contained sulfur, confirming a rather high anthropogenic impact on biogenic emissions and their oxidation processes. Among the sulfur-containing compounds, several organosulfates, nitrooxy organosulfates, and highly oxidized organosulfates (HOOS) were tentatively identified by high-resolution mass spectrometry. Correlations among HOOS, sulfate, and highly oxidized multifunctional organic compounds (HOMs) support the hypothesis of previous studies that HOOS are formed by reactions of gas-phase HOMs with particulate sulfate. Moreover, periods with high relative humidity indicate that aqueous-phase chemistry might play a major role in HOOS production. However, for dryer periods, coinciding signals for HOOS and gas-phase peroxyradicals (RO2•) were observed, suggesting RO2• to be involved in HOOS formation.

Complementary mass spectrometric techniques for the quantification of the protein corona: a case study on gold nanoparticles and human serum proteins.

Once nanoparticles enter a biological system, it is known that their surface is instantly covered by the biomolecules present with preference to proteins. This protein corona has been a subject of numerous studies in order to reveal its composition. Besides that, growing interest exists in its quantitative determination in order to gain a deeper insight into the nature of these nanoparticle-protein bioconjugates. Only a few analytical methods are available nowadays, so the aim of this study is to provide a reliable and alternative methodology for the quantification of the protein corona. The suggested approach is based on the assumption that the total protein content within the corona can be correlated to its sulfur concentration due to the presence of cysteine and methionine as sulfur-containing amino acids. Once the most abundant proteins had been identified with the use of gel electrophoresis with subsequent peptide analysis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS), the isolated nanoparticle-protein conjugates were subjected to total analysis of sulfur and the corresponding metal being present in the nanoparticles by inductively coupled plasma-mass spectrometry (ICP-MS). The concept is exemplarily demonstrated on citrate-stabilized gold nanoparticles (GNPs) incubated with human serum. Two different purification procedures were tested in order to isolate the sought bioconjugates. 26 most abundant proteins could be identified and an average of approximately 40 S atoms per protein was calculated and used for further studies. ICP-MS analyses of S/Au ratios served for the quantification of the protein corona revealing an absolute number of proteins bound to the incubated GNPs. Two main results could be obtained for this specific system under the chosen experimental conditions: the number of proteins per GNP decreased with their size from 10 nm to 60 nm and the obtained values suggested that the protein corona in this specific case was theoretically formed either as a monolayer (60 nm GNPs) or as a multilayer (5-7 protein layers per 10 nm GNP). Studies with bovine serum albumin (BSA) as the model protein showed similar results.

Using complementary mass spectrometric approaches for the determination of methylprednisolone metabolites in human urine

The metabolism of methylprednisolone is revisited in order to find new metabolites that could be important for distinguishing between different routes of administration. Recently developed liquid chromatography/tandem mass spectrometry (LC/MS/MS) strategies for the detection of corticosteroid metabolites have been applied to the study of methylprednisolone metabolism. The structures of these metabolites were studied using two complementary mass spectrometric techniques: LC/MS/MS in product ion scan mode with electrospray ionization and gas chromatography/mass spectrometry (GC/MS) in full scan mode with electron ionization. Metabolites were also isolated by semipreparative liquid chromatography fractionation. Each fraction was divided into two aliquots; one was studied by LC/MS/MS and the other by GC/MS after methoxyamine-trimethylsilyl derivatization. The combination of all the structural information allowed us to propose a comprehensive picture of methylprednisolone metabolism in humans. Overall, 15 metabolites including five previously unreported compounds have been detected. Specifically, 16β,17α,21-trihydroxy-6α-methylpregna-1,4-diene-3,11,20-trione, 17α,20β,21-trihydroxy-6α-methylpregna-1,4-diene-3, 11-dione, 11β,17α,21-trihydroxy-6α-hydroxymethylpregna-1,4-diene-3,20-dione, 11β,17α,20ξ,21-tetrahydroxy-6α-hydroxymethylpregna-1,4-diene-3-one, and 17α,21-dihydroxy-6α-hydroxymethylpregna-1,4-diene-3,11,20-trione are proposed as feasible structures for the novel metabolites. In addition to the expected biotransformations: reduction of the C20 carbonyl, oxidation of the C11 hydroxy group, and further 6β-hydroxylation, we propose that hydroxylation of the 6α-methyl group can also take place. New metabolites have been identified in urine samples collected after oral administration of 40 mg of methylprednisolone. All identified metabolites were found in all samples collected up to 36 h after oral administration. However, after topical administration of 5 g of methylprednisolone aceponate, neither the parent compound nor any of the metabolites were detected.

Metallomics investigations on potential binding partners of methylmercury in tuna fish muscle tissue using complementary mass spectrometric techniques

In this study, the binding behaviour of methylmercury (MeHg(+)) towards proteins is investigated. Free sulfhydryl groups in cysteine residues are known to be the most likely binding partners, due to the high affinity of mercury to sulphur. However, detailed knowledge about discrete binding sites in living organisms has been so far scarce. A metallomics approach using different methods like size-exclusion chromatography (SEC) and liquid chromatography (LC) coupled to inductively coupled plasma-mass spectrometry (ICP-MS) as well as complementary mass spectrometric techniques (electrospray ionisation-tandem mass spectrometry, ESI-MS/MS) are combined to sequence and identify possible target proteins or peptides after enzymatic digestion. Potential targets for MeHg(+) in tuna fish muscle tissue are investigated using the certified reference material CRM464 as a model tissue. Different extraction procedures appropriate for the extraction of proteins are evaluated for their efficiency using isotope dilution analysis for the determination of total Hg in the extracts. Due to the high chemical stability of the mercury-sulphur bond, the bioconjugate can be quantitatively extracted with a combination of tris(hydroxymethyl)aminomethane (TRIS) and sodium dodecyl sulphate (SDS). Using different separation techniques such as SEC and SDS-polyacrylamide gel electrophoresis (SDS-PAGE) it can be shown that major binding occurs to a high-molecular weight protein (M(w) > 200 kDa). A potential target protein, skeletal muscle myosin heavy chain, could be identified after tryptic digestion and capillary LC-ESI-MS/MS.

Application of complementary mass spectrometric techniques to the identification of ketoprofen phototransformation products

Ketoprofen (KP) is a nonsteroidal anti-inflammatory drug, which during UV irradiation rapidly transforms into benzophenone derivatives. Such transformation products may occur after topical application of KP, which is then exposed to sunlight resulting in a photo-allergic reaction. These reactions are mediated by the benzophenone moiety independently of the amount of allergen. The same reactions will also occur during wastewater or drinking water treatment albeit their effect in the aqueous environment is yet to be ascertained. In addition, only a few such transformation products have been recognised. To enable the detection and structural elucidation of the widest range of KP transformation products, this study applies complementary chromatographic and mass spectrometric techniques including gas chromatography coupled to single quadrupole or ion trap mass spectrometry and liquid chromatography hyphenated with quadrupole-time-of-flight mass spectrometry. Based on structural information gained in tandem and multiple MS experiments, and on highly accurate molecular mass measurements, chemical structures of 22 transformation products are proposed and used to construct an overall breakdown pathway. Among the identified transformation products all but two compounds retained the benzophenone moiety--a result, which raises important issues concerning the possible toxic synergistic effects of KP and its transformation products. These findings trigger further research into water treatment technologies that would limit their entrance into environmental or drinking waters.

Comparison of MALDI-TOF/MS and LC-QTOF/MS methods for the identification of enteric bacteria

Two complementary mass spectrometric techniques were evaluated for their applicability as methods for foodborne pathogen characterization, biomarker candidate discovery and identification. Ten clinical isolates of closely related organisms, Escherichia coli, Shigella sonnei and Shigella flexneri, were chosen for this study. Whole cell lysates were analyzed using both matrix assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF/MS) and liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF/MS). Evaluation of isolate mass spectra revealed unique protein profile patterns and potential biomarkers capable of species and sub-species identification. Strengths of each MS method, in addition to their advantages over traditional methods, are highlighted and a brief discussion of their potential as standard tools in the laboratory is presented.

Increased Confidence in Large-Scale Phosphoproteomics Data by Complementary Mass Spectrometric Techniques and Matching of Phosphopeptide Data Sets

Large-scale phosphoproteomics studies are of great interest due to their potential for the dissection of signaling pathways controlled by protein kinases. Recent advances in mass spectrometry (MS)-based phosphoproteomic techniques offer new opportunities to profile protein kinase activities in a comprehensive manner. However, this increasingly used approach still poses many analytical challenges. On one hand, high stringency criteria for phosphopeptide identification based on MS/MS data are needed in order to avoid false positives; however, on the other hand, these stringent criteria also result in the introduction of many false negatives. In the current report, we employ different mass spectrometric techniques for large-scale phosphoproteomics in order to reduce the presence of false negatives and enhance data confidence. A LTQ-Orbitrap LC-MS/MS platform identified approximately 3 times more phosphopeptides than Q-TOF LC-MS/MS instrumentation (4308 versus 1485 identifications, respectively). In both cases, collision induced dissociation (CID) was used to fragment peptides. Interestingly, the two platforms produced complementary data as many of the low scoring phosphopeptide ions identified by LTQ-Orbitrap MS/MS gave rise to high score identifications by Q-TOF MS/MS analysis, and vice versa. In fact, approximately 450 phosphopeptides identified by the Q-TOF instrument were not identified by the LTQ-Orbitrap. Further data comparison revealed the extent of the problem: in one experiment, the estimated number of false negatives (1066) was close to the number of identified phosphopeptides (1485). This work demonstrates that by using standard procedures for phosphopeptide identification the number of false negatives can be even greater than the number of false positives. We propose using historical phosphoproteomic data and spectral matching algorithms in order to efficiently minimize false negative rates.

Degradation of Ionized OV(OCH3)3in the Gas Phase. From the Neutral Compound All the Way down to the Quasi-terminal Fragments VO+and VOH+

The consecutive fragmentation of ionized trimethyl vanadate(V), OV(OCH3)3 (1), is examined by experiment and theory. After an elimination of formaldehyde from the molecular ion 1+, subsequent dissociations proceed via losses of first H2 and then two molecules of formaldehyde to finally yield the VOH+ cation; these redox reactions involve the V(II)/V(IV) manifold. At elevated energies, expulsion of CH3O* from 1+ can efficiently compete to afford OV(OCH3)2+, a formal V(V) compound, from which subsequent losses of H2 and two units of CH2O lead to bare VO+, thereby exploring the V(III)/V(V) redox manifold. Experiments using complementary mass spectrometric techniques, i.e., neutralization-reionization experiments and ion/molecule reactions, in conjunction with extensive computational studies provide deep insight into the ion structures and the relative energetics of these dissociation reactions. In particular, a quantitative energetic scheme is obtained that ranges from neutral OV(OCH3)3 all the way down to the quasi-terminal fragment ions VOH+ and VO+, respectively.

Complementary mass spectrometric techniques to achieve complete sequence coverage of recombinant human tropoelastin

Complementary mass spectrometric techniques to achieve complete sequence coverage of recombinant human tropoelastin

Mass spectrometric characterization of human skin elastin peptides produced by proteolytic digestion with pepsin and thermitase

This study investigated peptides resulting from the digestion of human skin elastin with pepsin and thermitase. Characterization of the peptides was performed using two complementary mass spectrometric techniques; LC/ESI-ion trap and nano-ESI-qTOF MS. 155 different peptides were identified using a combined database based and de novo sequencing approach resulting in a total sequence coverage of 65.4% calculated on the basis of the precursor tropoelastin (accession number A32707). A potential hydroxylation was found in 29% of the recovered prolines. Furthermore, the absence of amino acids expressed by exon 26A could be confirmed. However, contrary to earlier studies, amino acids expressed by exon 22 seem to exist.

Proteomic Analysis of Cleavage Events Reveals a Dynamic Two-step Mechanism for Proteolysis of a Key Parasite Adhesive Complex

The transmembrane micronemal protein MIC2 and its partner M2AP comprise an adhesive complex that is required for rapid invasion of host cells by the obligate intracellular parasite Toxoplasma gondii. Recent studies have shown that the MIC2/M2AP complex undergoes extensive proteolytic processing on the parasite surface during invasion, including primary processing of M2AP by unknown proteases and proteolytic shedding of the complex by an anonymous protease called MPP1. While it was shown that MPP1-mediated cleavage is necessary for efficient invasion, it remained unclear whether the adhesive complex was liberated by juxtamembrane or intramembrane proteolysis. Here, using a three-phase strategy of assigning cleavage sites based on intact matrix-assisted laser desorption/ionization mass followed by confirmation by enzymatic digestion and inhibitor profiling, we demonstrate that M2AP is processed by two parasite-derived proteases called MPP2 and MPP3. We also define the substrate repertoire of MPP2 by two-dimensional differential gel electrophoresis using fluorescent tags. Finally, we use complementary mass spectrometric techniques to unequivocally show that MIC2 is shed by intramembrane cleavage within its anchoring domain. Based on the properties of this cleavage site, we conclude that the sheddase, MPP1, is likely a multipass membrane protease of the Rhomboid family. Our data support a novel two-step proteolysis model that includes primary processing of the MIC2/M2AP complex followed by secondary cleavage to shed the complex from the parasite surface during the final steps of invasion.