Use of PASEF for Accelerated Protein Sequence Confirmation and De Novo Sequencing with High Data Quality.

Biopharmaceutical sequences can be well confirmed by multiple protease digests-e.g., trypsin, elastase, and chymotrypsin-followed by LC-MS/MS data analysis. High quality data can be used for de novo sequencing as well. PASEF (Parallel Accumulation and Serial Fragmentation) on the timsTOF instrument has been used to accelerate proteome and protein sequence studies and increase sequence coverage concomitantly.Here we describe the protein chemical and LC-MS methods in detail to generate high quality samples for sequence characterization from only 3 digests. We applied PASEF to generate exhaustive protein sequence coverage maps by combination of results from the three enzyme digests using a short LC gradient. The data quality obtained was high and adequate for determining antibody sequences de novo.Nivolumab and dulaglutide were digested by 3 enzymes individually. For nivolumab, 94/94/90% sequence coverage and 86/84/85% fragment coverage were obtained from the individual digest analysis with trypsin/chymotrypsin/elastase, respectively. For dulaglutide, 96/100/90% sequence coverage and 92/90/83% fragment coverage were obtained. The merged peptide map from the 3 digests for nivolumab resulted in ∼550 peptides; enough to safely confirm the full sequences and to determine the nivolumab sequence de novo.

Ionization of many-electron atoms by the action of two plasma models.

The Hartree-Fock equations for many-electron atoms embedded in a plasma medium are solved using two different plasma models: (a) Debye-Hückel screening (DHS) potential and (b) exponential cosine screened Coulomb (ECSC) potential. Roothaan's approach is implemented for these models after solving the inherent difficulties to evaluate integrals where screening appears explicitly. A corresponding computer code was developed using the method of global basis sets (GBS). The reliability of this approach was verified by solving the Hartree-Fock equations through implementation of the finite-differences and finite-element grid methods and applied to two-electron atoms, yielding excellent agreement with the Roothaan-GBS (RGBS) method. The RGBS method was used to study the energy evolution and ionization threshold of several closed- and open-shell many-electron atoms embedded either in weak or strong DHS or ECSC plasma conditions. In all cases, a critical value of the screening length is obtained for which ionization is achieved, being systematically larger for DHS conditions, indicating the effect of a more repulsive ECSC potential. For He-like atoms in the ground state, we report a comprehensive set of accurate total energy data as a function of the screening constant using the Lagrange mesh method, which includes the electron correlation effects. The electron correlation energy is estimated using this data with reference to the RGBS estimates of energy as the Hartree-Fock energy. The variation of correlation energy as a function of screening constant under the different plasma potentials is rationalized in terms of a conjectured comparison theorem. Finally, a discussion on the effect of plasma strength on localization or delocalization of the electronic density derived from the RGBS method is presented in terms of changes in the Shannon entropy, yielding consistent results for delocalization close to the ionization threshold.

High Prevalence of Weight Gain in Childhood Brain Tumor Survivors and Its Association With Hypothalamic-Pituitary Dysfunction.

PURPOSE: Childhood brain tumor survivors (CBTS) are at risk for developing obesity, which negatively influences cardiometabolic health. The prevalence of obesity in CBTS may have been overestimated in previous cohorts because of inclusion of children with craniopharyngioma. On the contrary, the degree of weight gain may have been underestimated because of exclusion of CBTS who experienced weight gain, but were neither overweight nor obese. Weight gain may be an indicator of underlying hypothalamic-pituitary (HP) dysfunction. We aimed to study prevalence of and risk factors for significant weight gain, overweight, or obesity, and its association with HP dysfunction in a national cohort of noncraniopharyngioma and nonpituitary CBTS. METHODS: Prevalence of and risk factors for significant weight gain (body mass index [BMI] change ≥ +2.0 standard deviation score [SDS]), overweight, or obesity at follow-up, and its association with HP dysfunction were studied in a nationwide cohort of CBTS, diagnosed in a 10-year period (2002-2012), excluding all craniopharyngioma and pituitary tumors. RESULTS: Of 661 CBTS, with a median age at follow-up of 7.3 years, 33.1% had significant weight gain, overweight, or obesity. Of the CBTS between 4 and 20 years of age, 28.7% were overweight or obese, compared with 13.2% of the general population between 4 and 20 years of age. BMI SDS at diagnosis, diagnosis of low-grade glioma, diabetes insipidus, and central precocious puberty were associated with weight gain, overweight, or obesity. The prevalence of HP dysfunction was higher in overweight and obese CTBS compared with normal-weight CBTS. CONCLUSION: Overweight, obesity, and significant weight gain are prevalent in CBTS. An increase in BMI during follow-up may be a reflection of HP dysfunction, necessitating more intense endocrine surveillance.

Peak Filtering, Peak Annotation, and Wildcard Search for Glycoproteomics.

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, e.g., HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges: finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra. Here, we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, e.g., at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, e.g., ± 0.01 Da. Also, new is glycan "wildcard" search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally, the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.

Strange semimetal dynamics in SrIrO3.

The interplay of electronic correlations, multi-orbital excitations, and spin-orbit coupling is a fertile ground for new states of matter in quantum materials. Here, we report on a polarized Raman scattering study of semimetallic SrIrO3. The momentum-space selectivity of Raman scattering allows to circumvent the challenge to resolve the dynamics of charges with very different mobilities. The Raman responses of both holes and electrons display an electronic continuum extending far beyond the energies allowed in a regular Fermi liquid. Analyzing this response within a memory function formalism, we extract their frequency dependent scattering rate and mass enhancement, from which we determine their DC-mobilities and electrical resistivities that agree well with transport measurement. We demonstrate that its charge dynamics is well described by a marginal Fermi liquid phenomenology, with a scattering rate close to the Planckian limit. This demonstrates the potential of this approach to investigate the charge dynamics in multi-band systems.

Assessment of biosimilarity under native and heat-stressed conditions: rituximab, bevacizumab, and trastuzumab originators and biosimilars.

Biosimilars are highly similar to, but not identical with, their originator products. As a result, structural differences between originators and biosimilars can be difficult to detect and characterize without the appropriate analytical tools. Therefore, we first focus on identifying initial structural differences between rituximab, bevacizumab, and trastuzumab originator and biosimilar pairs and later address how these differences change after applying thermal stress at 40 °C with orbital shaking for 4 weeks. Prior to incubation, we detected comparable secondary and tertiary structures for each pair and identified different levels of soluble aggregates, charge variants, and molecular weight variants due to differences in glycoforms and the number of C-terminal lysine groups. Over the course of incubation, we compared differences in charge variants and unfolding patterns. Taken together, our study provides a comparability exercise, providing information on the minor differences present between originator and biosimilar products and how those differences are impacted by stress.

Multifaceted assessment of rituximab biosimilarity: The impact of glycan microheterogeneity on Fc function.

Biosimilars are poised to reduce prices and increase patient access to expensive, but highly effective biologic products. However, questions still remain about the degree of similarity and scarcity of information on biosimilar products from outside of the US/EU in the public domain. Thus, as an independent entity, we performed a comparative analysis between the innovator, Rituxan® (manufactured by Genentech/Roche), and a Russian rituximab biosimilar, Acellbia® (manufactured by Biocad). We evaluated biosimilarity of these two products by a variety of state-of-the-art analytical mass spectrometry techniques, including tandem MS mapping, HX-MS, IM-MS, and intact MS. Both were found to be generally similar regarding primary and higher order structure, though differences were identified in terms of glycoform distribution levels of C-terminal Lys, N-terminal pyroGlu, charge variants and soluble aggregates. Notably, we confirmed that the biosimilar had a higher level of afucosylated glycans, resulting in a stronger FcγIIIa binding affinity and increased ADCC activity. Taken together, our work provides a comprehensive comparison of Rituxan® and Acellbia®.

Drops That Change Their Mind: Spontaneous Reversal from Spreading to Retraction.

A liquid drop may spread faster on surfaces when surfactants are added. Here we show that after some time the spreading in such systems can, under certain conditions, spontaneously reverse to retraction and the droplet pulls itself back, receding from areas it has just recently wetted, elevating its center of mass in a jerklike motion. The duration from drop placement to the onset of retraction ranges from hours to less than a second primarily as a function of surfactant concentration. When the retraction is asymmetric, it results in drop motion, and when it is symmetric, the mass of the drop collects itself on its spot. This phenomenon, which was predicted theoretically in 2014, is apparently a general one for drops with surfactants; however, other factors, such as evaporation and contamination, prevented its observance so far.

Differential Quantitative Determination of Site-Specific Intact N-Glycopeptides in Serum Haptoglobin between Hepatocellular Carcinoma and Cirrhosis Using LC-EThcD-MS/MS.

Intact N-glycopeptide analysis remains challenging due to the complexity of glycopeptide structures, low abundance of glycopeptides in protein digests, and difficulties in data interpretation/quantitation. Herein, we developed a workflow that involved advanced methodologies, the EThcD-MS/MS fragmentation method and data interpretation software, for differential analysis of the microheterogeneity of site-specific intact N-glycopeptides of serum haptoglobin between early hepatocellular carcinoma (HCC) and liver cirrhosis. Haptoglobin was immunopurified from 20 µL of serum in patients with early HCC, liver cirrhosis, and healthy controls, respectively, followed by trypsin/GluC digestion, glycopeptide enrichment, and LC-EThcD-MS/MS analysis. Identification and differential quantitation of site-specific N-glycopeptides were performed using a combination of Byonic and Byologic software. In total, 93, 87, and 68 site-specific N-glycopeptides were identified in early HCC, liver cirrhosis, and healthy controls, respectively, with high confidence. The increased variety of N-glycopeptides in liver diseases compared to healthy controls was due to increased branching with hyper-fucosylation and sialylation. Differential quantitation analysis showed that 5 site-specific N-glycopeptides on sites N184 and N241 were significantly elevated in early HCC compared to cirrhosis ( p < 0.05) and normal controls ( p ≤ 0.001). The result demonstrates that the workflow provides a strategy for detailed profiles of N-glycopeptides of patient samples as well as for relative quantitation to determine the level changes in site-specific N-glycopeptides between disease states.

A new comparison theorem on Hellmann potential.

Using some basic inequalities, the spherical Hellmann potential is assigned its place in the hierarchy of relative ordering, within the set of standard screened Coulomb potentials at all radial distances. The previously known comparison theorem applicable to the screened Coulomb potentials is thereby expanded to ascertain the relative ordering of energy levels for nℓ-states of Hellmann potential vis-a-vis those corresponding to the screened Coulomb potentials. The analytic results are supported by numerical calculation.

Parsimonious Charge Deconvolution for Native Mass Spectrometry.

Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new "parsimonious" charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies.

Structural, magnetic and electronic properties of pulsed-laser-deposition grown SrFeO3-δ thin films and SrFeO3-δ /La2/3Ca1/3MnO3 multilayers.

We studied the structural, magnetic and electronic properties of [Formula: see text] (SFO) thin films and [Formula: see text]/[Formula: see text] [Formula: see text]MnO3 (LCMO) superlattices that have been grown with pulsed laser deposition (PLD) on [Formula: see text] [Formula: see text] [Formula: see text] [Formula: see text] [Formula: see text] (LSAT) substrates. X-ray reflectometry and scanning transmission electron microscopy (STEM) confirm the high structural quality of the films and flat and atomically sharp interfaces of the superlattices. The STEM data also reveal a difference in the interfacial layer stacking with a SrO layer at the LCMO/SFO and a LaO layer at the SFO/LCMO interfaces along the PLD growth direction. The x-ray diffraction (XRD) data suggest that the as grown SFO films and SFO/LCMO superlattices have an oxygen-deficient [Formula: see text] structure with I4/ mmm space group symmetry ([Formula: see text]). Subsequent ozone annealed SFO films are consistent with an almost oxygen stoichiometric structure ([Formula: see text]). The electronic and magnetic properties of these SFO films are similar to the ones of corresponding single crystals. In particular, the as grown [Formula: see text] films are insulating whereas the ozone annealed films are metallic. The magneto-resistance effects of the as grown SFO films have a similar magnitude as in the single crystals, but extend over a much wider temperature range. Last but not least, for the SFO/LCMO superlattices we observe a rather large exchange bias effect that varies as a function of the cooling field.

Biosimilarity under stress: A forced degradation study of Remicade® and Remsima™.

Remsima™ (infliximab) is the first biosimilar monoclonal antibody (mAb) approved by the European Medical Agency and the US Food and Drug Administration. Remsima™ is highly similar to its reference product, Remicade®, with identical formulation components. The 2 products, however, are not identical; Remsima™ has higher levels of soluble aggregates, C-terminal lysine truncation, and fucosylated glycans. To understand if these attribute differences could be amplified during forced degradation, solutions and lyophilized powders of the 2 products were subjected to stress at elevated temperature (40-60°C) and humidity (dry-97% relative humidity). Stress-induced aggregation and degradation profiles were similar for the 2 products and resulted in loss of infliximab binding to tumor necrosis factor and FcγRIIIa. Appearances of protein aggregates and hydrolysis products were time- and humidity-dependent, with similar degradation rates observed for the reference and biosimilar products. Protein powder incubations at 40°C/97% relative humidity resulted in partial mAb unfolding and increased asparagine deamidation. Minor differences in heat capacity, fluorescence, levels of subvisible particulates, deamidation and protein fragments were observed in the 2 stressed products, but these differences were not statistically significant. The protein solution instability at 60°C, although quite significant, was also similar for both products. Despite the small initial analytical differences, Remicade® and Remsima™ displayed similar degradation mechanisms and kinetics. Thus, our results show that the 2 products are highly similar and infliximab's primary sequence largely defines their protein instabilities compared with the limited influence of small initial purity and glycosylation differences in the 2 products.

Detection and Measurement of Methionine Oxidation in Proteins.

Methionine oxidation is a prevalent modification found in proteins both in biological settings and in the manufacturing of biotherapeutic molecules. In cells, the oxidation of specific methionine sites can modulate protein function or promote interactions that trigger signaling pathways. In biotherapeutic development, the formation of oxidative species could be detrimental to the efficacy or safety of the drug product. Thus, methionine oxidation is a critical quality attribute that needs to be monitored throughout development. Here we describe a method using LC/MS/MS to identify site-specific methionine modifications in proteins. Antibodies are stressed with hydrogen peroxide, and the level of Met oxidation is compared to that of reference molecules. The protocols presented here are not specific to methionine and can be used more generally to identify other PTM risk sites in molecules after various types of treatments. © 2017 by John Wiley & Sons, Inc.

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery.

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests. Graphical Abstract ᅟ.

Fecal Nutrients Suggest Diets of Higher Fiber Levels in Free-Ranging than in Captive Proboscis Monkeys (Nasalis larvatus).

Understanding the natural diet of species may provide useful information that can contribute to successful captive maintenance. A common problem experienced with captive foregut-fermenting primate (colobine) diets is that they are deficient in fiber and therefore highly digestible. This may contribute to gastrointestinal disorders often observed in zoos. An approach to obtain information relevant for the improvement of diets is to compare the nutrient composition of feces from free-ranging and captive individuals. In theory, fecal material can be considered a proxy for diet intake integrated over a certain period of time. We collected fecal samples from eight free-ranging proboscis monkey (Nasalis larvatus, a highly endangered colobine species) groups from a secondary forest along the Kinabatangan River and four from a mixed mangrove-riverine forest along the Garama River, Sabah, Borneo, Malaysia. We also collected fecal samples from 12 individual captive adult/sub-adult proboscis monkeys from three different zoos. We confirmed that feces from free-ranging monkeys contained more fiber and less metabolic fecal nitrogen than those from captive specimens, indicating a less digestible diet in the wild. Modifying the diets of captive colobines to include more fiber, comparable to those of free-ranging ones, may contribute to their health and survival.

High variability in baseline urinary free cortisol values in patients with Cushing's disease.

OBJECTIVE: Twenty-four-hour urinary free cortisol (UFC) sampling is commonly used to evaluate Cushing's syndrome. Because there are few data on UFC variability in patients with active Cushing's disease, we analysed baseline UFC in a large patient cohort with moderate-to-severe Cushing's disease and assessed whether variability correlates with hypercortisolism severity. These data will help clinicians establish the minimum number of UFC samples required to obtain reliable data. DESIGN: Observational study (enrolment phase of Phase III study). METHODS: Patients (n = 152) with persistent/recurrent or de novo Cushing's disease and mean UFC (mUFC) ≥1·5×ULN (normal: 30-145 nmol/24 h) were included. Mean UFC level was calculated from four 24-h urine samples collected over 2 weeks. RESULTS: Over 600 24-h UFC samples were analysed. The mUFC levels of samples 1 and 2 and samples 3 and 4 were 1000 nmol/24 h (SD 1872) and 940 nmol/24 h (SD 2148), respectively; intrapatient coefficient of variation (CV) was 38% for mUFC. The intrapatient CV using all four samples was 52% (95% CI: 48-56). The intrapatient CV was 51% (95% CI: 44-58) for samples 1 and 2, 49% (95% CI: 43-56) for samples 3 and 4 and 54% (95% CI: 49-59) for samples 1, 2 and 3. Variability in mUFC increased as UFC levels increased. There were no correlations between UFC and clinical features of hypercortisolism. CONCLUSIONS: There is intrapatient variability of approximately 50% in 24-h UFC measurements, which is relevant to targets set to estimate any treatment effect. Analysing more than two 24-h collection periods in individual patients does not result in a relevant decrease in variability. Interestingly, UFC levels did not correlate with hypercortisolism severity.

Spinal cord transection before scoliosis correction in myelomeningocele may improve bladder function.

AIMS: In patients with myelomeningocele (MMC) and coexistent scoliosis, a spinal cord transection (SC-transection) is sometimes performed before scoliosis correction to prevent traction on the myelum after stretching the spinal column. Performing a SC-transection may have positive effects on bladder function, especially in case of refractory detrusor-sphincter dyssynergia. This study investigates the effects of SC-transection on lower and upper urinary tract outcomes. METHODS: All children with MMC who underwent scoliosis correction (1989-2009) were retrospectively reviewed. Cases were defined as those who underwent a SC-transection before scoliosis correction, whereas the control group comprised children who had a scoliosis correction alone. Urodynamic and clinical outcomes were examined. RESULTS: A total of 7 cases and 13 controls were identified. Postoperatively, compared to the control group, cases had relatively more often improvement of compliance (improvement in 6/7 vs. 9/13) and bladder capacity (improvement in 6/7 vs. 8/13). No effect of SC-transection was found on incontinence severity, clean intermittent catheterization frequency, use of antimuscarinic drugs, or signs of renal damage on ultrasound. CONCLUSIONS: SC-transection before scoliosis correction in children with MMC without lower extremity function, may improve bladder function with respect to bladder compliance and bladder capacity. Changes in symptoms or renal ultrasound were not found. No harmful effects of SC-transection were found, indicating that this procedure can be performed safely with respect to bladder function in these patients. Whether or not SC-transection should be recommended during scoliosis correction in patients with MMC to improve bladder function requires further study.

The influence of fining agents on the removal of some pesticides from white wine of Vitis vinifera L. cv. Emir.

The influences of fining agents (activated carbon, casein, kieselsol-gelatine, bentonite and polyvinylpolypyrrolidone) and their doses (low, middle, high) on the removal of six pesticides used in viticulture (vinclozolin, penconazole, α-endosulfan, imazalil, nuarimol and tetradifon) from white wine were investigated. The pesticides were added into white wine obtained from the Emir grape, and then the wine was clarified with the use of fining agents at low, middle and high doses. After the fining, extraction of pesticides from the wine was made by liquid-liquid extraction. Quantification and identification were performed by the multiresidual method using GC-MS and GC-ECD techniques. The effect of the fining agents on these pesticides ranged from little to large. Of the fining agents, activated carbon showed the largest effect on the removal of pesticides. The pesticide removal efficiencies of the fining agents were in the following order: activated carbon, casein, bentonite and kieselsol-gelatine. Polyvinylpolypyrrolidone (PVPP) had the least effect on the removal of pesticides. A linear relation was not found between fining agent doses and the amount of removed pesticides. α-Endosulfan, penconazole, imazalil and tetradifon were removed by the fining agents at the highest levels. Vinclozolin and nuarimol were the pesticides least affected, except activated carbon and casein.

Modeling the biomass growth and enzyme secretion by the white rot fungus Phanerochaete chrysosporium: a stochastic-based approach.

The white rot fungus Phanerochaete chrysosporium has been identified to be an environmentally useful microorganism for the degradation of various hazardous pollutants, mainly because of its ligninolytic enzyme system, particularly the lignin peroxidase (LiP) secreted by the fungus. In the present work, the behavior of the fungus in liquid medium due to variation in physico-chemical parameters, i.e., glucose concentration, nitrogen concentration, agitation, etc., was studied. Increment of the initial concentration of glucose in the medium increases the biomass growth and LiP activity, when cultured under controlled conditions. The biomass growth and LiP activity by the fungus was modeled following stochastic approach. The behavior of growth and enzyme activity of the fungus observed from the model were found to be in agreement with the experiments qualitatively.