A Longitudinal Pilot Study of Stress and Sleep in First-Year Osteopathic Medical Students.

OBJECTIVE: Poor sleep quality is thought to be a contributor to medical student stress. The authors evaluated the effect of high and low periods of academic stress on sleep quality and quantity in first-year medical students. METHODS: A group of 25 students in their first year of medical school were provided Fitbit Charge 3 activity trackers for continual use and were surveyed at 4 intervals to assess stress level, sleep quantity, and sleep quality. Fitbit data were collected through the Fitbit mobile app and uploaded to the Fitabase (Small Steps Labs, LLC) server. Data collection times were scheduled around the academic exam schedule. Weeks in which testing occurred were identified as high-stress periods. Results from assessments were compared to nontesting periods of low stress. RESULTS: During stressful periods, students slept an average of one hour less per 24-h period, took more naps, and reported poorer sleep quality than during the low-stress periods. No significant change was seen in the 4 surveyed intervals in sleep efficiency or sleep stages. CONCLUSION: Students slept less and had poorer quality sleep in their main sleep event during stressful periods but attempted to compensate with increased napping and weekend catchup sleep. The objective Fitbit activity tracker data were consistent with and validated the self-reported survey data. Activity trackers could potentially be used to optimize the efficiency and quality of both student napping and main sleep events as one component of a stress reduction program for medical students.

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS.

The detection, correlation, and comparison of peptide and product ions from a data independent LC-MS acquisition strategy with data dependent LC-MS/MS is described. The data independent mode of acquisition differs from an LC-MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan-to-scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge-state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC-MS/MS and data-independent, alternate scanning LC-MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data-independent LC-MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC-MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC-MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC-MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time-aligned data from data-independent alternate scanning LC-MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor-product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.

Quadrupole-time-of-flight mass spectrometer modified for higher-energy dissociation reduces protein assemblies to peptide fragments.

The gas-phase dissociation of protein assemblies is becoming crucial for the application of mass spectrometry to structural biology. However certain aspects of the dissociation mechanism remain elusive. Moreover, many protein complexes resist dissociation at the energies accessible with current instrumentation. Here we report new insights into the collision-induced dissociation mechanism of protein assemblies. By holding activation energy constant and varying the charge state of the precursor ion, we show that the total charge of the precursor ion dramatically influences the internal energy required to dissociate monomers from the protein assembly. Furthermore, we have developed a modified quadrupole-time-of-flight instrument capable of accessing activation energies higher than previously possible. Under these conditions, protein assemblies eject subunits with excess internal energy that subsequently fragment into peptides. Together, these data indicate that the non-covalent dissociation is limited by the amount of charge available and not merely the activation energy, and they project the exciting possibility of extracting sequence information directly from intact protein complexes in the gas phase.

Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry.

The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with (15)N and uniformly with (13)C. The pattern of isotope labeling of second-generation fragment ions derived via a(n) and b(n) ions (where n = 4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b(n) ions where n = 8 or 9.

Evidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry.

Tandem mass spectrometry (MS/MS) of peptides plays a key role in the field of proteomics, and an understanding of the fragmentation mechanisms involved is vital for data interpretation. Not all the fragment ions observed by low-energy collision-induced dissociation of protonated peptides are readily explained by the generally accepted structures for a- and b-ions. The possibility of a macrocyclic structure for b-type ions has been recently proposed. In this study, we have undertaken investigations of linear protonated YAGFL-NH(2), N-acetylated-YAGFL-NH(2), and cyclo-(YAGFL) peptides and their fragments using a combination of ion mobility (IM) separation and mass spectrometry. The use of IM in this work both gives insight into relative structural forms of the ion species and crucial separation of isobaric species. Our study provides compelling evidence for the formation of a stable macrocyclic structure for the b(5) ion generated by fragmentation of protonated linear YAGFL-NH(2). Additionally we demonstrate that the a(4) ion fragment of protonated YAGFL-NH(2) has at least two structures; one of which is attributable to a macrocyclic structure on the basis of its subsequent fragmentation. More generally, this work emphasizes the value of combined IM-MS/MS in probing the detailed fragmentation mechanisms of peptide ions, and illustrates the use of combined ion mobility/collisional activation/mass spectrometry analysis in achieving an effective enhancement of the resolution of the mobility separator.

Monitoring copopulated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry.

The precise mechanism of protein folding remains elusive and there is a deficiency of biophysical techniques that are capable of monitoring the individual behavior of copopulated protein conformers during the folding process. Herein, an ion mobility spectrometry (IMS) device integrated with electrospray ionization mass spectrometry (ESI-MS) has been used to successfully separate and analyze protein conformers differing in cross section and/or charge state. In an initial test, an ensemble of folded and partially folded conformers of the protein cytochrome c was separated. A detailed study undertaken on the amyloidogenic protein beta(2)-microglobulin (beta(2)m), which forms fibrils by protein unfolding followed by self-aggregation and is responsible for the disease dialysis-related amyloidosis, has generated important insights into its folding landscape. Initially, a systematic titration of beta(2)m over the pH range 2 to 7 using ESI-IMS-MS allowed individual conformers to be monitored and quantified throughout the acid denaturation process. Furthermore, a comparison of wild-type beta(2)m with single and double amino acid variants with a range of folding stabilities and propensities for amyloid fibril formation has provided illuminating evidence of the role of different conformers in protein stability and amyloidogenic aggregation. The ESI-IMS-MS data presented here not only demonstrate an important and informative further dimension to ESI-MS, but also illustrate the potential of the ESI-IMS-MS technique for unravelling protein folding enigmas in general and studying protein misfolding diseases in particular.

Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site.

BACKGROUND: Glutaminyl cyclase (QC) forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP) and mutated the apparent active site residues to assess their role in QC catalysis. RESULTS: The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence of the disulfide. Mutagenesis of the six active site residues present in both 1AMP and QC reveal essential roles for the two histidines (140 and 330, QC numbering) and the two glutamates (201 and 202), while the two aspartates (159 and 248) appear to play no catalytic role. ICP-MS analysis shows less than stoichiometric zinc (0.3:1) in the purified enzyme. CONCLUSIONS: We conclude that human pituitary glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site residues. In contrast to the aminopeptidase, however, QC does not appear to require zinc for enzymatic activity.

Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALDI Q-TOF) mass spectrometry and its implications for protein identification.

A study has been undertaken to evaluate the usefulness of MALDI Q-TOF data for protein identification. The comparison of MS data of protein digests obtained on a conventional MALDI TOF instrument to the MS data from the MALDI Q-TOF reveal peptide patterns with similar intensity ratios. However, comparison of MS/MS Q-TOF data produced by nanoelectrospray versus MALDI reveals striking differences. Peptide fragment ions obtained from doubly charged precursors produced by nanoelectrospray are mainly y-type ions with some b-ions in the lower mass range. In contrast, peptide fragment ions produced from the singly charged ions originating from the MALDI source are a mixture of y-, b- and a-ions accompanied by ions resulting from neutral loss of ammonia or water. The ratio and intensity of these fragment ions is found to be strongly sequence dependent for MALDI generated ions. The singly charged peptides generated by MALDI show a preferential cleavage of the C-terminal bond of acidic residues aspartic and glutamic acid and the N-terminal bond of proline. This preferential cleavage can be explained by the mobile proton model and is present in peptides that contain both arginine and an acidic amino acid. The MALDI Q-TOF MS/MS data of 24 out of 26 proteolytic peptides produced by trypsin or Asp-N digestions were successfully used for protein identification via database searching, thus indicating the general usefulness of the data for protein identification. De novo sequencing using a mixture of 160/18O water during digestion has been explored and de novo sequences for a number of peptides have been obtained.

A survey of educational uses of molecular visualization freeware.

As biochemists, one of our most captivating teaching tools is the use of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. Participants (n = 116) were asked to complete 11 multiple choice and 3 open ended questions. To provide more depth to these results, interviews were conducted with 12 of the participants. Many common themes arose in the survey and the interviews: a shared passion for the use of molecular visualization in teaching, broad diversity in software preference, the lack of uniform standards for assessment, a desire for more quality resources, and the challenge of enabling students to incorporate visualization in their learning. The majority of respondents had used molecular visualization for more than 5 years and mentioned 32 different visualization tools used, with Jmol and PyMOL clearly standing out as the most frequently used programs at the present time. The most common uses of molecular visualization in teaching were lecture and lab illustrations, followed by exam questions, in-class or in-laboratory exercises, and student projects, which frequently included presentations. While a minority of instructors used a grading rubric/scoring matrix for assessment of student learning with molecular visualization, many expressed a desire for common use assessment tools.

Molecular characterization of tick salivary gland glutaminyl cyclase.

Glutaminyl cyclase (QC) catalyzes the cyclization of N-terminal glutamine residues into pyroglutamate. This post-translational modification extends the half-life of peptides and, in some cases, is essential in binding to their cognate receptor. Due to its potential role in the post-translational modification of tick neuropeptides, we report the molecular, biochemical and physiological characterization of salivary gland QC during the prolonged blood feeding of the black-legged tick (Ixodes scapularis) and the gulf-coast tick (Amblyomma maculatum). QC sequences from I. scapularis and A. maculatum showed a high degree of amino acid identity to each other and other arthropods and residues critical for zinc binding/catalysis (D159, E202, and H330) or intermediate stabilization (E201, W207, D248, D305, F325, and W329) are conserved. Analysis of QC transcriptional gene expression kinetics depicts an upregulation during the bloodmeal of adult female ticks prior to fast-feeding phases in both I. scapularis and A. maculatum suggesting a functional link with bloodmeal uptake. QC enzymatic activity was detected in saliva and extracts of tick salivary glands and midguts. Recombinant QC was shown to be catalytically active. Furthermore, knockdown of QC transcript by RNA interference resulted in lower enzymatic activity, and small, unviable egg masses in both studied tick species as well as lower engorged tick weights for I. scapularis. These results suggest that the post-translational modification of neurotransmitters and other bioactive peptides by QC is critical to oviposition and potentially other physiological processes. Moreover, these data suggest that tick-specific QC-modified neurotransmitters/hormones or other relevant parts of this system could potentially be used as novel physiological targets for tick control.

Effect of somatosensory stimulation of two and three nerves on upper limb function in healthy individuals.

BACKGROUND AND PURPOSE: Improvement in motor function has been reported in healthy subjects following somatosensory stimulation (SS) of individual upper limb peripheral nerves. This effect could have beneficial applications in rehabilitation, but there is little knowledge of the effects of stimulating multiple upper limb nerves. This study evaluated the effects of SS of two and three nerves on hand function. METHODS: A single blind within-group repeated measures design was utilized. Ten healthy subjects (27.1 ± 5.4 years [mean ± SD], three men) were recruited and, after a familiarization session, were given SS to the ipsilateral hand in a randomized order to two (ulnar and median) and three (ulnar, median and radial) nerves on two occasions separated by at least one week. The time required to complete the Jebsen-Taylor Hand Function Test (JTHFT) and handgrip strength of the ipsilateral hand were measured before and immediately after each SS session. RESULTS: Total JTHFT time decreased significantly by an average of 3.58 ± 2.75 s (9.9%; P = 0.003) and 4.10 ± 3.20 s (11.6%; P = 0.003) following SS to two and three nerves, respectively, but no difference between the two was found. Handgrip strength decreased significantly by 1.82 ± 1.91 kgf (P = 0.015) following SS to three nerves only. CONCLUSIONS: This study suggests that SS of three nerves may facilitate motor training but may also induce a reduction in muscle performance. Further studies are needed to determine the clinical implications of these findings for neurological rehabilitation.

Ion mobility augments the utility of mass spectrometry in the identification of human hemoglobin variants.

The global dispersion of hemoglobin variants through population migration has precipitated a need for their identification. A particularly effective mass spectrometry (MS)-based procedure involves analysis of the intact globin chains in diluted blood to detect the variant through mass anomalies, followed by location of the variant amino acid residue by direct analysis of the enzymatically digested globins. Here we demonstrate the use of ion mobility separation in combination with this MS procedure to reduce mass spectral complexity. In one example, the doubly charged tryptic peptide from a low abundance variant (4%) occurred at the same m/z value as a singly and a doubly charged interfering ion. In another example, the singly charged tryptic peptide from an alpha-chain variant (26%) occurred at the same m/z value as a doubly charged interfering ion. Ion mobility was used to separate the variant ions from the interfering ions, thus allowing the variant peptides to be observed and sequenced by tandem mass spectrometry.

Generation of end-group information from polyethers by matrix-assisted laser desorption/ionisation collision-induced dissociation mass spectrometry.

A series of polyethers, namely poly(ethylene glycol) (PEG), poly(propylene glycol) (PPG), poly(butylene glycol) (PBG) and poly(tetramethylene glycol) (PTMeG), has been characterised by means of matrix-assisted laser desorption/ionisation collision-induced dissociation (MALDI-CID) using a hybrid sector orthogonal-time-of-flight (TOF) instrument. The data indicate that this technique can be used to generate information about the end-group functionality of these polymers, including in some cases information about branching of the alkyl chains of the initiating groups. Proposals are made for the fragmentation pathways for these polymers.

Direct analysis of pharmaceutical drug formulations using ion mobility spectrometry/quadrupole-time-of-flight mass spectrometry combined with desorption electrospray ionization.

A novel approach to the rapid analysis of pharmaceutical drug formulations using hyphenated ion mobility spectrometry (IMS) and time-of-flight mass spectrometry (ToF-MS) that requires no sample pretreatment or chromatographic separation is described. A modified quadrupole time-of-flight mass spectrometer containing an ion mobility drift cell was used for gas-phase electrophoretic separation of ions prior to ToF-MS detection. The generation of sample ions directly from tablets and cream formulations was effected by desorption electrospray ionization (DESI) using a modified electrospray ion source. The analysis of a range of over-the-counter and prescription tablet formulations is described, including histamine H2 receptor antagonist (ranitidine), analgesic (paracetamol), opiate (codeine), and aromatase inhibitor anticancer (anastrozole) drugs. The successful determination of active drugs from soft formulations, such as an antiseptic cream (chlorhexidine) and a nicotine-containing skin patch, is also presented. Limits of detection for the active drugs using the DESI/IMS/ToF-MS method fell within the high-picomole to nanomole range. In all cases, the use of ion mobility drift tube separation showed increased selectivity for active drug responses (present as low as 0.14% w/w) over excipient responses such as poly(ethylene glycol). Tandem mass spectrometric analysis of precursor ions separated by IMS allowed positive confirmation of active drugs with little loss of ion mobility efficiency. The ability to analyze hard or soft pharmaceutical formulations directly by DESI combined with ion mobility spectrometry/mass spectrometry in approximately 2 min demonstrates the potential applicability of this novel method to pharmaceutical screening of low-molecular-weight drug formulations with high selectivity over the formulation vehicle.

Evidence for macromolecular protein rings in the absence of bulk water.

We have examined the architecture of a protein complex in the absence of bulk water. By determining collision cross sections of assemblies of the trp RNA binding protein, TRAP, we established that the 11-membered ring topology of the complex can be maintained within a mass spectrometer. We also found that the binding of tryptophan enhances the stability of the ring structure and that addition of a specific RNA molecule increases the size of the complex and prevents structural collapse. These results provide definitive evidence that protein quaternary structure can be maintained in the absence of bulk water and highlight the potential of ion mobility separation for defining shapes of heterogeneous macromolecular assemblies.

Human pituitary glutaminyl cyclase: expression in insect cells and dye affinity purification.

Human pituitary glutaminyl cyclase (hQC) was expressed in Drosophila S2 cells under the control of an inducible metallothionene promoter and fused to the Drosophila immunoglobulin-binding protein signal sequence to enable secretion into the culture media. Expression levels reached 50 microg/mL culture media after 7 days of induction. The enzyme was purified to homogeneity directly from culture media by affinity chromatography on Reactive Blue 4-agarose using a step pH elution. The identity of the expressed protein was confirmed by peptide mass mapping and Western blotting. Glutaminyl cyclase was expressed as a fully active 37 kDa enzyme with kcat/Km values of 14.3, 9.3, and 2.4 mM(-1)s(-1) for the substrates Gln-Gln, Gln-NH(2), and Gln-t-butyl ester, respectively. The two cysteines were disulfide bonded, and the lone predicted glycosylation site, asparagine 49, was shown by both enzymatic deglycosylation of the expressed enzyme and site-directed mutagenesis to be glycosylated.

Applications of a travelling wave-based radio-frequency-only stacked ring ion guide.

The use of radio-frequency (RF)-only ion guides for efficient transport of ions through regions of a mass spectrometer where the background gas pressure is relatively high is widespread in present instrumentation. Whilst multiple collisions between ions and the background gas can be beneficial, for example in inducing fragmentation and/or decreasing the spread in ion energies, the resultant reduction of ion axial velocity can be detrimental in modes of operation where a rapidly changing influx of ions to the gas-filled ion guide needs to be reproduced at the exit. In general, the RF-only ion guides presently in use are based on multipole rod sets. Here we report investigations into a new mode of ion propulsion within an RF ion guide based on a stack of ring electrodes. Ion propulsion is produced by superimposing a voltage pulse on the confining RF of an electrode and then moving the pulse to an adjacent electrode and so on along the guide to provide a travelling voltage wave on which the ions can surf. Through appropriate choice of the travelling wave pulse height, velocity and gas pressure it will be shown that the stacked ring ion guide with the travelling wave is effective as a collision cell in a tandem mass spectrometer where fast mass scanning or switching is required, as an ion mobility separator at pressures around 0.2 mbar, as an ion delivery device for enhancement of duty cycle on an orthogonal acceleration time-of-flight (oa-TOF) mass analyser, and as an ion fragmentation device at higher wave velocities.