Discovery of RSV-Induced BRD4 Protein Interactions Using Native Immunoprecipitation and Parallel Accumulation-Serial Fragmentation (PASEF) Mass Spectrometry.

Respiratory Syncytial Virus (RSV) causes severe inflammation and airway pathology in children and the elderly by infecting the epithelial cells of the upper and lower respiratory tract. RSV replication is sensed by intracellular pattern recognition receptors upstream of the IRF and NF-κB transcription factors. These proteins coordinate an innate inflammatory response via Bromodomain-containing protein 4 (BRD4), a protein that functions as a scaffold for unknown transcriptional regulators. To better understand the pleiotropic regulatory function of BRD4, we examine the BRD4 interactome and identify how RSV infection dynamically alters it. To accomplish these goals, we leverage native immunoprecipitation and Parallel Accumulation-Serial Fragmentation (PASEF) mass spectrometry to examine BRD4 complexes isolated from human alveolar epithelial cells in the absence or presence of RSV infection. In addition, we explore the role of BRD4's acetyl-lysine binding bromodomains in mediating these interactions by using a highly selective competitive bromodomain inhibitor. We identify 101 proteins that are significantly enriched in the BRD4 complex and are responsive to both RSV-infection and BRD4 inhibition. These proteins are highly enriched in transcription factors and transcriptional coactivators. Among them, we identify members of the AP1 transcription factor complex, a complex important in innate signaling and cell stress responses. We independently confirm the BRD4/AP1 interaction in primary human small airway epithelial cells. We conclude that BRD4 recruits multiple transcription factors during RSV infection in a manner dependent on acetyl-lysine binding domain interactions. This data suggests that BRD4 recruits transcription factors to target its RNA processing complex to regulate gene expression in innate immunity and inflammation.

What do you need to know about mass spectrometry? A brief guide for endocrinologists.

In routine hormonology, liquid chromatography mass spectrometry (LCMS) is now an established technique for androgen, urinary cortisol and metanephrine assay. It has the undeniable advantage of great analytical specificity, but with sensitivity that clearly depends on financial investment in a very high-end spectrometer. We describe the general principles of LCMS and the routine applications so far developed in hormonology. The purpose is to familiarise endocrinologists with the techniques under development and their pros and cons.

Medical Devices; Immunology and Microbiology Devices; Classification of the Mass Spectrometer System for Clinical Use for the Identification of Microorganisms. Final order.

The Food and Drug Administration (FDA or we) is classifying the mass spectrometer system for clinical use for the identification of microorganisms into class II (special controls). The special controls that apply to the device type are identified in this order and will be part of the codified language for the mass pectrometer system for clinical use for the identification of microorganisms' classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

Medical Devices; Clinical Chemistry and Clinical Toxicology Devices; Classification of the Total 25-Hydroxyvitamin D Mass Spectrometry Test System. Final order.

The Food and Drug Administration (FDA, the Agency, or we) is classifying the total 25-hydroxyvitamin D mass spectrometry test system into class II (special controls). The special controls that apply to the device type are identified in this order and will be part of the codified language for the total 25-hydroxyvitamin D mass spectrometry test system's classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

LC-MS characterization of valsartan degradation products and comparison with LC-PDA

abstract Valsartan was submitted to forced degradation under acid hydrolysis condition as prescribed by the ICH. Degraded sample aliquots were separated via HPLC using a Hypersil ODS (C18) column (250 x 4.6 mm i.d., 5 µm). Either photodiode array (PDA) detection or mass spectrometry (MS) full scan monitoring of HPLC runs were used. HPLC-PDA failed to indicate Valsartan degradation under forced acid degradation, showing an insignificant peak area variation and that Valsartan apparently remained pure. HPLC-MS using electrospray ionization (ESI) and total ionic current (TIC) monitoring did not reveal any peak variation either, but inspection of the ESI mass spectra showed the appearance of m/z 306 and m/z 352 ions for the same retention time as that of Valsartan (m/z 436). These ions were identified as being protonated molecules of two co-eluting degradation products formed by hydrolysis. These assignments were confirmed by ESI-MS/MS with direct infusion of the degraded samples. The results showed that the use of selective HPLC-MS is essential for monitoring Valsartan degradation. Efficient HPLC separation coupled to selective and structural diagnostic MS monitoring seems therefore mandatory for comprehensive drug degradation studies, particularly for new drugs and formulations, and for method development.

resumo Valsartana (VAL) foi submetida à degradação forçada em meio ácido conforme procedimento descrito no ICH. Os produtos de degradação (PDs) foram monitorados ao longo do tempo de degradação pela técnica de Cromatografia Líquida (LC) utilizando uma coluna Hypersil ODS (C18) (250 x 4,6 mm d.i., 5 µm). A detecção foi feita com dois detectores: espectrofotométrico (PDA) e espectrometria de massas (MS) por corrente iônica total. Ambas as técnicas falharam na identificação dos PDs obtidos ao longo do monitoramento, mostrando insignificantes variações na área do pico e permanecendo com pureza de pico ao longo de toda a eluição. Somente depois da avaliação por íon extraído (XIC), foi possível observar o aumento do íon m/z 306 e m/z 352 exatamente no mesmo tempo de retenção do íon molecular (m/z 436). Estes resultados mostram um caso simples e didático em que somente o uso de um método seletivo de LC-MS pode ser utilizado para monitorar produtos de degradação. Neste trabalho, é apresentado um caso real em que a separação por LC deve ser acoplada a métodos seletivos obtidos por MS, especialmente no estudo de PDs para novos fármacos, formulações e no desenvolvimento de métodos.

Mass spectrometry-based serum and plasma peptidome profiling for prediction of treatment outcome in patients with solid malignancies.

INTRODUCTION: Treatment selection tools are needed to enhance the efficacy of targeted treatment in patients with solid malignancies. Providing a readout of aberrant signaling pathways and proteolytic events, mass spectrometry-based (MS-based) peptidomics enables identification of predictive biomarkers, whereas the serum or plasma peptidome may provide easily accessible signatures associated with response to treatment. In this systematic review, we evaluate MS-based peptide profiling in blood for prompt clinical implementation. METHODS: PubMed and Embase were searched for studies using a syntax based on the following hierarchy: (a) blood-based matrix-assisted or surface-enhanced laser desorption/ionization time-of-flight MS peptide profiling (b) in patients with solid malignancies (c) prior to initiation of any treatment modality, (d) with availability of outcome data. RESULTS: Thirty-eight studies were eligible for review; the majority were performed in patients with non-small cell lung cancer (NSCLC). Median classification prediction accuracy was 80% (range: 66%-93%) in 11 models from 14 studies reporting an MS-based classification model. A pooled analysis of 9 NSCLC studies revealed clinically significant median progression-free survival in patients classified as "poor outcome" and "good outcome" of 2.0 ± 1.06 months and 4.6 ± 1.60 months, respectively; median overall survival was also clinically significant at 4.01 ± 1.60 months and 10.52 ± 3.49 months, respectively. CONCLUSION: Pretreatment MS-based serum and plasma peptidomics have shown promising results for prediction of treatment outcome in patients with solid tumors. Limited sample sizes and absence of signature validation in many studies have prohibited clinical implementation thus far. Our pooled analysis and recent results from the PROSE study indicate that this profiling approach enables treatment selection, but additional prospective studies are warranted.

Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring.

New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.

In-depth qualitative and quantitative analysis of composite glycosylation profiles and other micro-heterogeneity on intact monoclonal antibodies by high-resolution native mass spectrometry using a modified Orbitrap.

Here, we describe a fast, easy-to-use, and sensitive method to profile in-depth structural micro-heterogeneity, including intricate N-glycosylation profiles, of monoclonal antibodies at the native intact protein level by means of mass spectrometry using a recently introduced modified Orbitrap Exactive Plus mass spectrometer. We demonstrate the versatility of our method to probe structural micro-heterogeneity by describing the analysis of three types of molecules: (1) a non-covalently bound IgG4 hinge deleted full-antibody in equilibrium with its half-antibody, (2) IgG4 mutants exhibiting highly complex glycosylation profiles, and (3) antibody-drug conjugates. Using the modified instrument, we obtain baseline separation and accurate mass determination of all different proteoforms that may be induced, for example, by glycosylation, drug loading and partial peptide backbone-truncation. We show that our method can handle highly complex glycosylation profiles, identifying more than 20 different glycoforms per monoclonal antibody preparation and more than 30 proteoforms on a single highly purified antibody. In analyzing antibody-drug conjugates, our method also easily identifies and quantifies more than 15 structurally different proteoforms that may result from the collective differences in drug loading and glycosylation. The method presented here will aid in the comprehensive analytical and functional characterization of protein micro-heterogeneity, which is crucial for successful development and manufacturing of therapeutic antibodies.

Large-molecule quantification: sensitivity and selectivity head-to-head comparison of triple quadrupole with Q-TOF.

BACKGROUND: Bioanalysts are continuously looking for innovative ideas or instruments to increase the sensitivity and selectivity of their assays. Research for better mass spectrometers is becoming crucial with the emerging trend of large-molecule quantification. This study lists the different advantages of high-resolution MS (HRMS) over standard triple quadrupole instruments and proposes basic guidelines on how to use HRMS for large-molecule quantification in a regulated environment. RESULTS: A direct comparison between HRMS and triple quadrupole instruments for the quantification of six different model peptides (desmopressin, calcitonin, enfuvirtide, exenatide, glucagon and somatostatin) was completed. The HRMS instrument, when used specifically for targeted quantification ('quant/quant'), showed equivalent or better sensitivity for all compounds tested. CONCLUSION: This paper demonstrates that the use of a HRMS instrument in a regulated environment is a viable technique for quantification of large molecules. The latter was able to allow flexibility and selectivity to adapt the specificity of each assay with sensitivity comparable to the triple quadrupole instrument.

Application of mass spectrometry to molecular diagnostics of viral infections.

Mass spectrometry (MS) has found numerous applications in life sciences. It has high accuracy, sensitivity and wide dynamic range in addition to medium- to high-throughput capabilities. These features make MS a superior platform for analysis of various biomolecules including proteins, lipids, nucleic acids and carbohydrates. Until recently, MS was applied for protein detection and characterization. During the last decade, however, MS has successfully been used for molecular diagnostics of microbial and viral infections with the most notable applications being identification of pathogens, genomic sequencing, mutation detection, DNA methylation analysis, tracking of transmissions, and characterization of genetic heterogeneity. These new developments vastly expand the MS application from experimental research to public health and clinical fields. Matching of molecular techniques with specific requirements of the major MS platforms has produced powerful technologies for molecular diagnostics, which will further benefit from coupling with computational tools for extracting clinical information from MS-derived data.

Using high-resolution quadrupole TOF technology in DMPK analyses.

Recent advances in quadrupole TOF (Q-TOF) MS have some bioanalytical scientists referring to a 'paradigm shift' in their field. They are speaking of a potential move away from workflows based upon triple-quadrupole MS. Gone would be the optimizing of numerous parameters in selected-reaction monitoring (SRM) experiments, replaced with more generic workflows provided by Q-TOF instruments with high data acquisition rates, excellent mass accuracy (≤5 ppm) and high resolving power (≥30,000). Such a move could pay real dividends for high-throughput workflows, especially in drug metabolism and pharmacokinetics analyses where quantitation and qualification studies could actually be merged. But, are modern Q-TOF-MS instruments, touted as high-resolution MS, ready for this? If not, how close is it? This article will examine these questions by reviewing recent advances in Q-TOF technology and some fascinating orthogonal technology (such as ion mobility) that modern Q-TOFs employ for even greater analytical power.

Selection of neutral losses and characteristic ions for mass spectral classifier.

Gas chromatography-mass spectrometry (GC-MS) is widely used in many fields because of its high sensitivity, high resolution and reproducibility. The major challenge of this analytical technology is the identification of components in complex samples. Generally, mass spectral library searching is commonly employed to assist in the identification of unknown spectra. However, this widely available method just provides a hit-list of candidates ordered by their numerical similarity indices. When an unknown compound has many isomeric compounds or is absent from the reference library, this approach might be less useful. Classification of mass spectra, a complementary technique to the library searching, is beneficial to computer-aided mass spectral interpretation but suffers from the fact that the variables used in the classifier are usually uninterpretable. In this study, a novel classifier is built based on data mining and feature analysis. In this classifier, the neutral loss is skillfully used to identify the differences between mass spectra of alcohols and ethers in the data set. After comparison with two chemometric methods, Fisher ratios linear discriminant analysis (LDA) and genetic algorithm partial least squares discriminant (GA-DPLS) analysis, it is found that our method achieves a better predictive ability. More importantly, this method is able to predict whether compounds could be classified correctly or not.

On the use of different mass spectrometric techniques for characterization of sequence variability in genomic DNA.

After completion of the human genome sequence the search for differences among individual genomes has become the centre of focus for geneticists. Two different types of polymorphism-single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs)-are major sources of genetic diversity and are of widespread use in genetic analysis. A plethora of genotyping techniques have been developed, and mass spectrometry (MS) is among the most widely used analytical platforms. The most striking advantage of mass spectrometric genotyping assays over others is the use of the measured molecular mass information for allele calling. The molecular mass is less error-prone than other sequence-specific parameters, including migration times, retention times, or hybridization yields, as it represents an intrinsic property of a nucleic acid molecule that is directly related to its nucleotide composition. Mass spectrometric assays can roughly be divided into two major groups-matrix-assisted laser desorption/ionization (MALDI)-based and electrospray ionization (ESI)-based assays. An important subdivision of ESI-based genotyping methods are approaches that originate from the hyphenation of liquid chromatography (LC) to MS. The principles of these three classes of mass spectrometric genotyping techniques are summarized in this review. Possibilities and limitations are critically discussed to assist scientists, especially non-experts in MS, in choosing the appropriate mass spectrometric assay for genotyping a genetic marker of interest. [figure: see text]

Characterization and identification of isomeric flavonoid O-diglycosides from genus Citrus in negative electrospray ionization by ion trap mass spectrometry and time-of-flight mass spectrometry.

Flavonoid O-diglycosides are important bioactive compounds from genus Citrus. They often occur as isomers, which makes the structural elucidation difficult. In the present study, the fragmentation behavior of six flavonoid O-diglycosides from genus Citrus was investigated using ion trap mass spectrometry in negative electrospray ionization (ESI) with loop injection. For the flavonoid O-rutinosides, [M-H-308]- ion was typically observed in the MS2 spectrum, suggesting the loss of a rutinose. The fragmentation patterns of flavonoid O-neohesperidosides were more complicated in comparison with their rutinoside analogues. A major difference was found in the [M-H-120]- ion in the MS2 spectrum, which was a common feature of all the flavonoid O-neohesperidosides. The previous literature for naringin located the loss of 120Da to the glycan part, whereas the present study for naringin had shown that the [M-H-120]- ion was produced by a retro-Diels-Alder reaction in ring C, and this fragmentation pattern was confirmed by the accurate mass measurement using an orthogonal time-of-flight mass spectrometer. Combined with high performance liquid chromatography (HPLC) and diode array detection (DAD), the established approach to the structural identification of flavonoid O-diglycosides by ion trap mass spectrometry was applied to the analysis of extracts of two Chinese medicines derived from genus Citrus, namely Fructus aurantii and F. aurantii immaturus. According to the HPLC retention behavior, the diagnostic UV spectra and the molecular structural information provided by multistage mass spectrometry (MS(n)) spectra, 13 flavonoid O-glycosides in F. aurantii and 12 flavonoid O-glycosides in F. a. immaturus were identified rapidly.

Integrated 2-D CE.

A simple methodology for converting a commercial CE-MS instrument into an integrated 2-D CE system has been developed. The first-dimensional capillary operates as a typical CE instrument with UV/visible detection. Fractions leaving the first dimension are automatically collected and introduced into the second dimension, performed on a CE-MS apparatus, for analysis. The integrated system allows fractions in the second dimension to be analyzed using various electrophoretic modes. As an example, in this work we performed the separation of two families of antibiotics (nitroimidazoles and tetracyclines) in the first dimension and the subsequent resolution of the antibiotics in each family (nitroimidazoles were resolved by MEKC and tetracyclines by CZE) in the second dimension. The proposed system, which operates in an highly automatic manner, is flexible and allows various combination of electrophoretic modes to be implemented. In addition, the use of a mass spectrometer detector in the second dimension further increases the analytical potential of the system as a result of the high selectivity and wealth of structural information provided by the MS detector.

Characterization of nucleic acid higher order structure by high-resolution tandem mass spectrometry.

Mass spectrometry (MS) is extensively used for the identification and sequencing of nucleic acids but has so far seen limited use for characterization of their higher order structures. Here, we have applied a range of different tandem mass spectrometry techniques, including electron detachment dissociation (EDD), infrared multiphoton dissociation (IRMPD), activated ion (AI) EDD, and EDD/IRMPD MS(3), in a Fourier transform ion cyclotron resonance mass spectrometer to the characterization of three isomeric 15mer DNAs with different sequences and predicted solution-phase structures. Our goal was to explore whether their structural differences could be directly probed with these techniques. We found that all three 15mers had higher order structures in the gas phase, although preferred structures were predicted for only two of them in solution. Nevertheless, EDD, AI EDD, and EDD/IRMPD MS(3) experiments yielded different cleavage patterns with less backbone fragmentation for the more stable solution-phase structure than for the other two 15mers. By contrast, no major differences were observed in IRMPD, although the extent of backbone cleavage was higher with that technique for all three 15mers. Thus, experiments utilizing the radical ion chemistry of EDD can provide complementary structural information compared to traditional slow heating methods, such as IRMPD, for structured nucleic acids.

Processing and classification of protein mass spectra.

Among the many applications of mass spectrometry, biomarker pattern discovery from protein mass spectra has aroused considerable interest in the past few years. While research efforts have raised hopes of early and less invasive diagnosis, they have also brought to light the many issues to be tackled before mass-spectra-based proteomic patterns become routine clinical tools. Known issues cover the entire pipeline leading from sample collection through mass spectrometry analytics to biomarker pattern extraction, validation, and interpretation. This study focuses on the data-analytical phase, which takes as input mass spectra of biological specimens and discovers patterns of peak masses and intensities that discriminate between different pathological states. We survey current work and investigate computational issues concerning the different stages of the knowledge discovery process: exploratory analysis, quality control, and diverse transforms of mass spectra, followed by further dimensionality reduction, classification, and model evaluation. We conclude after a brief discussion of the critical biomedical task of analyzing discovered discriminatory patterns to identify their component proteins as well as interpret and validate their biological implications.

Medical devices; clinical chemistry and clinical toxicology devices; classification of newborn screening test systems for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. Final rule.

The Food and Drug Administration (FDA) is classifying newborn screening test systems for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry into class II (special controls). The special control that will apply to the device is the guidance document entitled "Class II Special Controls Guidance Document: Newborn Screening Test Systems for Amino Acids, Free Carnitine, and Acylcarnitines Using Tandem Mass Spectrometry." The agency is taking this action in response to a petition submitted under the Federal Food, Drug, and Cosmetic Act (the act) as amended by the Medical Device Amendments of 1976, the Safe Medical Devices Act of 1990, the Food and Drug Administration Modernization Act of 1997, and the Medical Device User Fee and Modernization Act of 2002. The agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device. Elsewhere in this issue of the Federal Register, FDA is publishing a notice of availability of a guidance document that is the special control for this device.