A framework for quality control in quantitative proteomics

A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.

Dependence of human cell survival and proliferation on the CASP3 prodomain

Mechanisms that regulate cell survival and proliferation are important for both the development and homeostasis of normal tissue, and as well as for the emergence and expansion of malignant cell populations. Caspase-3 (CASP3) has long been recognized for its proteolytic role in orchestrating cell death-initiated pathways and related processes; however, whether CASP3 has other functions in mammalian cells that do not depend on its known catalytic activity have remained unknown. To investigate this possibility, we examined the biological and molecular consequences of reducing CASP3 levels in normal and transformed human cells using lentiviral-mediated short hairpin-based knockdown experiments in combination with approaches designed to test the potential rescue capability of different components of the CASP3 protein. The results showed that a ≥50% reduction in CASP3 levels rapidly and consistently arrested cell cycle progression and survival in all cell types tested. Mass spectrometry-based proteomic analyses and more specific flow cytometric measurements strongly implicated CASP3 as playing an essential role in regulating intracellular protein aggregate clearance. Intriguingly, the rescue experiments utilizing different forms of the CASP3 protein showed its prosurvival function and effective removal of protein aggregates did not require its well-known catalytic capability, and pinpointed the N-terminal prodomain of CASP3 as the exclusive component needed in a diversity of human cell types. These findings identify a new mechanism that regulates human cell survival and proliferation and thus expands the complexity of how these processes can be controlled. The graphical abstract illustrates the critical role of CASP3 for sustained proliferation and survival of human cells through the clearance of protein aggregates.

Characterizing the secretome of EGFR mutant lung adenocarcinoma

Background

Lung cancer is the leading cause of cancer related death worldwide, mainly due to the late stage of disease at the time of diagnosis. Non-invasive biomarkers are needed to supplement existing screening methods to enable earlier detection and increased patient survival. This is critical to EGFR-driven lung adenocarcinoma as it commonly occurs in individuals who have never smoked and do not qualify for current screening protocols.

Methods

In this study, we performed mass spectrometry analysis of the secretome of cultured lung cells representing different stages of mutant EGFR driven transformation, from normal to fully malignant. Identified secreted proteins specific to the malignant state were validated using orthogonal methods and their clinical activity assessed in lung adenocarcinoma patient cohorts.

Results

We quantified 1020 secreted proteins, which were compared for differential expression between stages of transformation. We validated differentially expressed proteins at the transcriptional level in clinical tumor specimens, association with patient survival, and absolute concentration to yield three biomarker candidates: MDK, GDF15, and SPINT2. These candidates were validated using ELISA and increased levels were associated with poor patient survival specifically in EGFR mutant lung adenocarcinoma patients.

Conclusions

Our study provides insight into changes in secreted proteins during EGFR driven lung adenocarcinoma transformation that may play a role in the processes that promote tumor progression. The specific candidates identified can harnessed for biomarker use to identify high risk individuals for early detection screening programs and disease management for this molecular subgroup of lung adenocarcinoma patients.

Magnetic resonance imaging of masticatory muscles in basset hounds

OBJECTIVES

To describe low- and high-field MRI characteristics of occult masticatory muscle lesions in basset hounds.

MATERIALS AND METHODS

Retrospective review of the MR images of the heads of 44 basset hounds that had been imaged for reasons unrelated to suspected muscle disease.

RESULTS

In most basset hounds, there was reduced bulk of the superficial part of the temporalis and masseter muscles together with bilaterally symmetrical T2W and T1W hyperintense signal with reduced contrast enhancement compared to normal muscle. Interpretation of various pulse sequences suggested that the affected muscle areas contained adipose tissue with no evidence of inflammation, and this was confirmed on biopsy in one dog. This pattern of changes is different from MRI changes in inflammatory myopathies.

CLINICAL SIGNIFICANCE

Poor muscle bulk and MRI signal changes in the superficial parts of the temporalis and masseter muscles in basset hounds appear to be normal findings in this breed and should not be misinterpreted as evidence of an inflammatory myopathy.

Metal Cationization Extractive Electrospray Ionization Mass Spectrometry of Compounds Containing Multiple Oxygens

Extractive electrospray ionization is an ambient ionization technique that allows real-time sampling of liquid samples, including organic aerosols. Similar to electrospray ionization, the composition of the electrospray solvent used in extractive electrospray ionization can easily be altered to form metal cationized molecules during ionization simply by adding a metal salt to the electrospray solvent. An increase in sensitivity is observed for some molecules that are lithium, sodium, or silver cationized compared with the protonated molecule formed in extractive electrospray ionization with an acid additive. Tandem mass spectrometry of metal cationized molecules can also significantly improve the ability to identify a compound. Tandem mass spectrometry of lithium and silver cationized molecules can result in an increase in the number and uniqueness of dissociation pathways relative to [M + H]⁺. These results highlight the potential for extractive electrospray ionization with metal cationization in analyzing complex aerosol mixtures. Graphical Abstract ᅟ.

Automated Trapping Column Exchanger for High-Throughput Nanoflow Liquid Chromatography

As compared to conventional high-performance liquid chromatography (HPLC) techniques, nanoflow HPLC exhibits improved sensitivity and limits of detection. However, nanoflow HPLC suffers from low throughput due to instrument failure (e.g., fitting fatigue and trapping column failure), limiting the utility of the technique for clinical and industrial applications. To increase the robustness of nanoflow HPLC, we have developed and tested a trapping column exchanging robot for autonomous interchange of trapping columns. This robot makes reproducible, automated connections between the active trapping column and the rest of the HPLC system. The intertrapping column retention time is shown to be sufficiently reproducible for scheduled selected reaction monitoring assays to be performed on different trapping columns without rescheduling the selection windows.

Miniature Flow-Through Low-Temperature Plasma Ionization Source for Ambient Ionization of Gases and Aerosols

The design and operation of an inexpensive, miniature low-temperature plasma ion source is detailed. The miniature low-temperature plasma ion source is operated in a "flow-through" configuration, wherein the gaseous or aerosolized analyte, caffeine or pyrolyzed ethyl cellulose, in a carrier gas is used as the plasma gas. In this flow-through configuration, the sensitivity for the caffeine standard and the pyrolysis products of ethyl cellulose is maintained or increased and the reproducibility of the ion source is increased. Changes in the relative intensity of ions from the aerosol produced by pyrolysis of ethyl cellulose are observed in the mass spectrum when the low-temperature plasma ion source is used in the flow-through configuration. Experiments suggest this change in relative intensity is likely due to differences in ionization efficiency rather than increased fragmentation of ethyl cellulose pyrolysis products during ionization. Flow-through low-temperature plasma ionization with the miniature ion source is shown to be a promising technique for the ionization of compounds in gases or aerosol particles.

Antimony(III)-D, L-tartrates exhibit proton-assisted enantioselective binding in solution and in the gas phase

The negative ion mode ESI mass spectral analysis of antimony(III)-D- and -L-tartrate ("tartar emetic"), in association with leucine enantiomeric isotopomers, revealed remarkable proton-assisted enantioselective molecular recognition phenomena. The current study infers that recognition of amino acids by antimony(III)-D,L-tartrate complexes requires that the chiral selector associate a proton to become enantioselective. The dianionic selector itself failed to show enantiomeric discrimination capacity. This observation was shown to be consistent both in solution-phase targeting full scan and gas-phase targeting collision threshold dissociation (CTD) experiments. Importantly, this disparity in enantioselective binding capacity between the dianionic and the protonated monoanionic representatives of antimony(III)-D- and -L-tartrates could only be clearly revealed by ESI-MS and tandem mass spectrometry experiments as described herein. This finding urges a more in-depth study of mechanisms associated with exhibited enantiomeric resolving capacity of antimony tartrates in HPLC and CE applications, as well as in former ESI-MS association studies.

Antiepithelial cell antibodies do not impair paediatric renal allograft survival but appear to be associated with acute viral infections

There is a reported association between antiepithelial cell (AEC) antibodies and increased renal allograft loss in paediatric recipients. Our unit experienced a dramatic fall in 1-year graft survival so we undertook a study to determine if AEC antibodies could account for such losses. We also studied healthy children and adults as well as a group of individuals with serologically proven viral infection in an attempt to determine the prevalence and possible aetiology of these antibodies. Sera were screened for AEC antibodies in a microcytotoxicity test using a lung epithelial cell line (A549) as target. The prevalence of these antibodies in our paediatric recipients was similar to that reported elsewhere but we found no correlation between the presence of AEC antibody and allograft loss. Within the control populations, we found the antibody was more prevalent in children than in adults (p < 0.0001). We also found a strong age banding pattern, with antibody being present in 50% of children under 10 years and declining with increasing age, so that by the age of 16 years the seroprevalence was similar to that found in our adults. However, AEC antibody had a significantly higher prevalence in individuals with active viral infection than in our healthy control groups (p = 0.00003). A positive association was noted between rubella and respiratory syncytial virus and AEC antibody presence and a negative association with varicella zoster. We conclude that AEC antibodies do not correlate with increased paediatric renal allograft loss but appear to be linked to certain viral infections.

Origin of porcine brain natriuretic peptide-like immunoreactive innervation of the middle cerebral artery in the rat

We recently demonstrated that porcine brain natriuretic peptide-like immunoreactive (pBNPir) fibers innervate parts of the cardiovascular system, including the arteries comprising the circle of Willis. To determine the origin of this innervation, we used the retrograde fluorescent tracer Fast Blue dye combined with pBNP immunocytochemistry. Cells which project to the middle cerebral artery and were also pBNPir were found in the trigeminal, pterygopalatine and superior cervical ganglia bilaterally but not in the geniculate or otic ganglia. The majority of these double-labelled cells were found in the ipsilateral trigeminal (46%) and superior cervical ganglia (34%). A pBNP-like substance may be a natural vasodilator in sympathetic, sensory and to a lesser extent parasympathetic neurons innervating the cerebrovascular system.

CNS projections to the pterygopalatine parasympathetic preganglionic neurons in the rat: a retrograde transneuronal viral cell body labeling study

The retrograde transneuronal viral cell body labeling method was used to study the CNS nuclei that innervate the parasympathetic preganglionic neurons which project to the pterygopalatine ganglion. Small injections of a suspension of pseudorabies virus (PRV) were made in the pterygopalatine ganglion of rats and after 4 days their brains wer e processed for immunohistochemical detection of PRV. Some of the tissues were stained with a dual immunofluoresence method that permitted the visualization of PRV and neurotransmitter enzyme or serotonin immunoreactivity in the same cell. Retrograde cell body labeling was detected in the ipsilateral ventrolateral medulla oblongata in the region that has been termed the superior salivatory nucleus. This area was the same region that was retrogradely labeled after Fluoro-Gold dye injections in the pterygopalatine ganglion. Retrograde transneuronally infected cell bodies that provide putative afferent inputs to the pytergopalatine parasympathetic preganglionic neurons were mapped throughout the brain. In the medulla oblongata, transneuronally labeled neurons were seen in the nucleus tractus solitarii, dorsomedial part of the spinal trigeminal nucleus and gigantocellular reticular nucleus. In most experiments, some A1 catecholamine cells and serotonin neurons of the raphe magnus, raphe pallidus, raphe obscurus, and parapyramidal nuclei were labeled. In the pons, labeled cells were found in the parabrachial nucleus. A5 catecholamine cell group, and non-catecholamine part of the subcoeruleus region. In the midbrain, cell body labeling was located in the central gray matter and retrorubral field. In the diencephalon, labeling was found mainly in the hypothalamus. The areas included the lateral hypothalamic area, lateral preoptic area, dorsomedial and paraventricular hypothalamic nuclei, and ventral zona incerta. Contralateral second order cell body labeling was seen in the tuberomammillary nucleus of the hypothalamus. Some of these cells were histidine decarboxylase-immunoreactive. In the forebrain, the bed nucleus of the stria terminalis, substantia innominata, and an area of the cerebral cortex called the amygdalopiriform transition zone were labeled.

L-glutamate mapping of cardioreactive areas in the rat posterior hypothalamus

The posterior hypothalamus has long been regarded as a CNS region that provides a sympatho-excitatory influence on the cardiovascular system and functions in thermoregulation as a heat-producing center. These ideas have been based on data derived from electrical stimulation and lesion experiments. These methods are now regarded as inadequate for accurate localization of CNS functions. In order to re-examine the function of the posterior hypothalamus, a chemical stimulation study was performed. Microinjections of the excitatory amino acid L-glutamate were made in the posterior hypothalamus of pentobarbital-anesthetized rats. This method was used in combination with autoradiography to localize [3H]glutamate, which was included with the injectate. No pressor responses were elicited from any site within the posterior hypothalamus. In contrast, chemical stimulation of the posterior periventricular hypothalamus produced large decreases in blood pressure (delta BP = 25 mm Hg) and in heart rate (delta HR = 30 bpm). Injections in the posterior hypothalamic nucleus elicited small reductions in blood pressure and heart rate. Injections in the dorsal hypothalamic area produced a similar small response. Injections ventral to the periventricular zone were also weakly reactive, but a significant elevation in rectal temperature was seen. To summarize, the most cardioresponsive area was within the periventricular zone caudal to the posterior hypothalamic nucleus and was situated near the fasciculus retroflexus.

Cardiovascular effects produced by L-glutamate stimulation of the lateral hypothalamic area

L-Glutamate microinjections into the tuberal region of the lateral hypothalamic area (LHAt) caused a fall in blood pressure and heart rate in pentobarbital-anesthetized rats. The bradycardia was mediated by both beta-adrenergic and muscarinic mechanisms as demonstrated with pharmacological blockade. The hypotension was due to a decrease in cardiac output, not a decrease in total peripheral resistance. In addition, there was a reduction in coronary blood flow. If heart rate was held constant by pharmacological blockade or by electrical cardiac pacing, L-glutamate stimulation of the LHAt still caused a fall in blood pressure. When the electrically paced model was used, this hypotension was due to a fall in cardiac output. In contrast, with the pharmacological blockade of the heart, the hypotension was due to a decrease in the total peripheral resistance. The cardiac output reduction in the paced condition was not mediated solely by either beta-sympathetic or parasympathetic mechanisms as determined by pharmacological blockade. With heart rate held constant by either drugs or pacing, LHAt stimulation did not alter regional blood flow or resistance in any vascular bed, including the coronary circulation. We conclude that L-glutamate stimulation of the LHAt lowers the cardiac output and heart rate by both parasympathetic and beta-adrenergic mechanisms and elicits hypotension by lowering cardiac output in the naive and electrically paced model.

L-glutamate stimulation of the zona incerta in the rat decreases heart rate and blood pressure

Microinjections of L-glutamate into the zona incerta of pentobarbital anesthetized rats caused decreases in blood pressure and heart rate. The bradycardic response was reduced by approximately 70% after i.v. administration of atropine methyl nitrate. After combined muscarinic and beta-adrenergic blockade the bradycardic response was reduced to 90% of the control value. This suggests that the bradycardia was mediated primarily by activating the vagal outflow. Blood pressure decreases elicited after pharmacological blockade of the heart with both atropine and timolol were approximately 50% of the control values. This indicates that the zona incerta is also capable of altering stroke volume and/or inhibiting the sympathetic outflow controlling the peripheral blood vessels. By using an injectate containing L-glutamate mixed with [3H]L-glutamate and subsequent analysis of autoradiographic tissue sections, we have determined that the most reactive site is the region of the ventral zona incerta.

Centrally administered bombesin modulates gastric motility

Intracerebroventricular bombesin alters arterial pressure and gastrointestinal transit in rats. In order to evaluate the influence of bombesin on arterial and gastric intraluminal pressure in a specific site in the central nervous system, we microinjected bombesin into the medial subnucleus of the nucleus tractus solitarius (mNTS) in 28 rats anesthetized with choralose. Bombesin (78 pmole in 25 nl), but not vehicle, caused an increase of tonic gastric intraluminal pressure (2.6 +/- 0.5 cm H2O) and of phasic gastric intraluminal pressures but did not acutely alter arterial pressure. The effect on tonic and phasic gastric intraluminal pressure was dose-dependent. The threshold dose was 7.8 pmole. Intravenous bombesin caused a similar dose-dependent rise in tonic gastric intraluminal pressure but did not significantly change the mean amplitude of phasic gastric intraluminal pressures. Transection of the cervical spinal cord and both cervical vagus nerves blocked the effect of centrally but not peripherally administered bombesin. We conclude that bombesin microinjected into the mNTS does not influence arterial pressure but does raise tonic and phasic gastric intraluminal pressures. Bombesin may act in the NTS as a central modulator of gastric motility.

Nonproduction of toxic shock syndrome toxin 1 by coagulase-negative staphylococci

We tested 187 strains of coagulase-negative staphylococci (CNS) for the production of toxic shock syndrome toxin 1 (TSST-1). A total of 111 CNS strains were isolated from the tampons of menstruating women and 74 were isolated from unused tampons. Two strains were isolated from the genital tract of a patient with toxic shock syndrome. Strains were cultivated by the membrane-over-agar method to enhance production of TSST-1, and culture supernatants were tested by two exquisitely sensitive enzyme-linked immunosorbent assays. None of the 187 CNS strains produced TSST-1. We conclude that CNS colonizing the genital tracts of menstruating women and unused tampons produce TSST-1 infrequently, if ever, and are unlikely to play a role in toxic shock syndrome.

Chorea-amyotrophy with chronic hemolytic anemia: a variant of chorea-amyotrophy with acanthocytosis

We studied two siblings with chorea and amyotrophy of adult onset and spherocytic hemolytic anemia. Autopsy revealed an atrophic striatum with iron deposition and spheroid bodies. Degeneration of the substantia nigra and spinal cord anterior horns was seen without iron deposition. The disorder seems to be a variant of the chorea-amyotrophy-acanthocytosis syndrome, and the pathology may account for evidence of parkinsonism and amyotrophy in that syndrome. Acanthocytosis may not be the only hematologic abnormality in this disorder.

Central modulation of gastric pressure by substance P: a comparison with glutamate and acetylcholine

We have sought to determine if changes in arterial and gastric pressure occurred with selective chemical stimulation of the dorsomedial NTS. Substance P (SP) and L-glutamate (L-glu), but not acetylcholine (ACh), elicited a dose-dependent decrease in tonic gastric pressure and inhibited gastric phasic activity. As previously reported, L-glu and ACh, but not SP elicited dose-dependent arterial hypotension. The data support a putative role for SP in visceral reflexes mediated by vagal nerves.

Modulation of gastric and arterial pressure by nucleus tractus solitarius in rat

By using L-glutamate as a physiological tool to selectively stimulate neurons in specific subnuclear regions of the nucleus tractus solitarius (NTS), we have sought to differentiate those regions that modulate cardiovascular activity from those that modulate gastric activity. Microinjections of L-glutamate (300 pmol/25 nl) into the dorsomedial NTS of alpha-chloralose-anesthetized rats elicited dose-dependent falls in arterial pressure (AP) of 37.5 +/- 7.7 Torr from a base line of 130 +/- 5.8 Torr and gastric pressure (GP) of 0.8 +/- 0.1 cmH2O and inhibited the usual 5-6 waves/min phasic activity. Microinjection into the ventromedial NTS did not affect AP but transiently lowered GP by 1.6 +/- 0.2 cmH2O and eliminated phasic waves. The GP changes were vagally mediated. Microinjections into the area postrema or the hypoglossal nucleus elicited neither AP nor GP changes. Microinjections in other NTS areas at the same rostral-caudal level did not alter GP consistently. This study suggests that local stimulation of neurons in a specific region of the NTS elicits vagally mediated alterations of tonic GP and phasic activity and that AP and GP can be influenced independently in the medial NTS region.

Pharmacologic effects of L-dopa are not closely linked temporally to striatal dopamine concentration

In an attempt to gain insight into the mechanism of the "long-term response" to L-dopa in parkinsonians, we studied the temporal relationship between turning behavior and striatal dopamine (DA) levels after L-dopa administration to rats with unilateral nigral lesions. Turning behavior peaked at 30 minutes (9.0 +/- 1.5 turns per rat per minute), diminished in intensity, reached a new peak (10.8 +/- 1) at 3 hours, and persisted for 280 minutes after L-dopa administration. In contrast, dopamine levels in the striatum ipsilateral to the lesion peaked at 20 minutes and returned to control levels by 90 minutes after L-dopa administration. These data suggest that behaviors elicited by an increase in brain (striatal) dopamine levels may persist long after the dopamine concentration has returned to control levels.

Altered pharmacokinetics of L-dopa metabolism in rat striatum deprived of dopaminergic innervation

Rats with unilateral lesions of the substantia nigra were treated with L-dopa 25 mg/kg subcutaneously 30 minutes after treatment with carbidopa 25 mg/kg intraperitoneally. In the ipsilateral striatum, dopamine levels achieved a peak of 1.57 +/- 0.63 micrograms/g (control 0.19 +/- 0.05 micrograms/g) at 20 minutes and did not differ from controls by 90 minutes after L-dopa administration. Dopamine levels peaked in the contralateral striatum at 45 minutes (11.96 +/- 0.14 micrograms/g, where control levels were 7.74 +/- 0.22 micrograms/g) and returned to control values by 180 minutes. These data suggest that in patients with advanced Parkinson's disease, L-dopa administration results in a smaller increase and a shorter duration of elevation in striatal dopamine concentration than in controls. These observations support the hypothesis that the "wearing-off" phenomenon that occurs during the treatment of patients with Parkinson's disease occurs as a consequence of a reduction in the rate of conversion of L-dopa to dopamine and perhaps diminished capacity for the storage of dopamine.