Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms

Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS2 data acquisition and more than doubling the number of proteoforms identified in previous studies.

Improved Label-Free Quantification of Intact Proteoforms Using Field Asymmetric Ion Mobility Spectrometry

The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high-performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here, we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF.

Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes

One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn2+ -containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.

Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy

The ability to map combinatorial patterns of post-translational modifications (PTMs) of proteins remains challenging for traditional bottom-up mass spectrometry workflows. There are also hurdles associated with top-down approaches related to limited data analysis options for heavily modified proteoforms. These shortcomings have accelerated interest in middle-down MS methods that focus on analysis of large peptides generated by specific proteases in conjunction with validated bioinformatics strategies to allow quantification of isomeric histoforms. Mapping multiple PTMs simultaneously requires the ability to obtain high sequence coverage to allow confident localization of the modifications, and 193 nm ultraviolet photodissociation (UVPD) has been shown to cause extensive fragmentation for large peptides and proteins. Histones are an ideal system to test the ability of UVPD to characterize multiple modifications, as the combinations of PTMs are the underpinning of the biological significance of histones and at the same time create an imposing challenge for characterization. The present study focuses on applying 193 nm UVPD to the identification and localization of PTMs on histones by UVPD and comparison to a popular alternative, electron-transfer dissociation (ETD), via a high-throughput middle-down LC/MS/MS strategy. Histone Coder and IsoScale, bioinformatics tools for verification of PTM assignments and quantification of histone peptides, were adapted for UVPD data and applied in the present study. In total, over 300 modified forms were identified, and the distributions of PTMs were quantified between UVPD and ETD. Significant differences in patterns of PTMs were found for histones from HeLa cells prior to and after treatment with a deacetylase inhibitor. Additional fragment ion types generated by UVPD proved essential for extensive characterization of the most heavily modified forms (>5 PTMs).

A new probe for detecting zinc-bound carbonic anhydrase in cell lysates and cells

We report the synthesis and application of a small molecule probe for carbonic anhydrase (CA) to track holo-CA in cell lysates and live-cell models of zinc dyshomeostasis. The probe displays a 12-fold increase in fluorescence upon binding to bovine CA and also responds to human CA isoforms.

Pinpointing Double Bond and sn-Positions in Glycerophospholipids via Hybrid 193 nm Ultraviolet Photodissociation (UVPD) Mass Spectrometry

Complete structural characterization of complex lipids, such as glycerophospholipids, by tandem mass spectrometry (MS/MS) continues to present a major challenge. Conventional activation methods do not generate fragmentation patterns that permit the simultaneous discernment of isomers which differ in both the positions of acyl chains on the glycerol backbone and the double bonds within the acyl chains. Herein we describe a hybrid collisional activation/UVPD workflow that yields near-complete structural information for glycerophospholipids. This hybrid MS3 strategy affords the lipid's sum composition based on the accurate mass measured for the intact lipid as well as highly specific diagnostic product ions that reveal both the acyl chain assignment (i.e., sn-position) and the site-specific location of double bonds in the acyl chains. This approach is demonstrated to differentiate sn-positional and double-bond-positional isomers, such as the regioisomeric phosphatidylcholines PC 16:0/18:1(n-9) and PC 18:1(n-9)/16:0, and has been integrated into an LC-MS3 workflow.

Modulation of Protein Fragmentation Through Carbamylation of Primary Amines

We evaluate the impact of carbamylation of the primary amines of the side-chains of Lys and the N-termini on the fragmentation of intact protein ions and the chromatographic properties of a mixture of E. coli ribosomal proteins. The fragmentation patterns of the six unmodified and carbamylated proteins obtained by higher energy collision dissociation (HCD) and ultraviolet photodissociation (UVPD) were compared. Carbamylation significantly reduced the total number of protons retained by the protein owing to the conversion of basic primary amines to non-basic carbamates. Carbamylation caused a significant negative impact on fragmentation of the protein by HCD (i.e., reduced sequence coverage and fewer diagnostic fragment ions) consistent with the mobile proton model, which correlates peptide fragmentation with charge distribution and the opportunity for charge-directed pathways. In addition, fragmentation was enhanced near the N- and C-termini upon HCD of carbamylated proteins. For LCMS/MS analysis of E. coli ribosomal proteins, the retention times increased by 16 min on average upon carbamylation, an outcome attributed to the increased hydrophobicity of the proteins after carbamylation. As noted for both the six model proteins and the ribosomal proteins, carbamylation had relatively little impact on the distribution or types of fragment ions product by UVPD, supporting the proposition that the mechanism of UVPD for intact proteins does not reflect the mobile proton model. Graphical Abstract ᅟ.

Documentation of pain assessment and treatment: how are we doing?

The purpose of this analysis was to evaluate documentation of practice provided by a multidisciplinary team of nurses, physicians, and pharmacists who participated in an educational program on postoperative pain management. Chart audit of 787 patient charts at 6 sites revealed documentation of pain histories in approximately 75% of the charts, most often in the surgeon's history and physical examination. Examination of multiple assessment items indicated that the experimental group, relative to the control group, experienced an increase of more than 10% in the documentation of pain intensity, pain quality, pain duration, numeric rating scale used, pain behavior, factors that increase pain, vital signs, sedation level, cognitive status, social interaction, and mood from before the program to 6 months after the program. Across all sites, documentation of assessment, treatment, and treatment outcome data was infrequent and inconsistent. Calculation of documentation of 4 items that constituted a focused assessment of postoperative pain on the surgical floor revealed a significant program effect for assessment of pain quality and pain intensity. A postprogram survey of participants in the educational program revealed an increase in discussion of postoperative pain management with other practitioners and an increase in use of a 0 to 10 scale to rate pain. More documentation of patient pain history, clinical problems, treatment, and follow-up action is needed to improve practice and research.

Surgical patients' fear of addiction to pain medication: the effect of an educational program for clinicians

OBJECTIVE

The appropriate and optimal use of analgesics is essential for the adequate management of postoperative pain. Concern that use of opioid analgesics contributes to the development of addiction is a barrier to effective pain relief. The purpose of this study was to determine the prevalence of fear of addiction in postoperative patients in relation to surgical outcomes and staff participation in an educational program.

DESIGN

Two treatment levels (program vs. control) and three data collection periods (before program, immediately after the program, and 6 months after the program).

SETTING

Six community hospitals with 100-500-bed capacities in a southeastern state.

PATIENTS

Seven hundred eighty-seven patients who had undergone orthopedic or laparotomy procedures.

INTERVENTIONS

Staff at three of the six hospitals received an educational program to promote implementation of Agency for Health Care Policy and Research acute pain management guidelines.

OUTCOME MEASURES

Patient report of preoperative and postoperative fear of addiction, satisfaction with pain treatment, communication with clinicians, and pain intensity.

RESULTS

Only 10.8% of the sample reported preoperative or postoperative fear of addiction. Staff participation in the educational program was found to decrease fear of addiction in this sample. Fear of addiction was also related to surgery type, with disc surgery patients more likely to report fear of addiction as compared with patients undergoing other types of surgery. Fear of addiction was not related to other outcomes in this sample.

CONCLUSIONS

Fear of addiction is not prevalent among postoperative patients, yet clinician education can further decrease the proportion of surgical patients who fear of addiction to pain medication.

Clinical economics: calculating the cost of acute postoperative pain medication

Few data are available that address the cost of postoperative pain management, although such knowledge would enhance our understanding of caregiver choices related to direct medical costs, such as type, frequency, and route of medication. This article describes the cost of postoperative pain medications before and after an educational program provided to nurses, pharmacists, and physicians in six community hospitals. Medication costs were calculated by averaging across all brands the average wholesale price of the most common dose administered in the sample for each medication. The median cost of postoperative pain medication across all days, all surgeries, was $9.46. Calculating the cost of acute postoperative pain medication suggested that cost over stay is highly influenced by the use of a few expensive medications. The relationship of medication cost to length of stay (LOS), function, and pain intensity is discussed.

An evaluation of facial expression displayed by patients with chest pain

OBJECTIVE

To determine whether patterns of facial expressions of patients complaining of chest pain can aid in the diagnosis of myocardial infarctions.

DESIGN

Exploratory.

SETTING

Southeastern university medical center emergency department (ED).

PATIENTS

Twenty-eight patients in the ED who presented with chest pain. Age range was 40 to 84 years, with a mean of 65.4 years.

OUTCOME MEASURES

Common patterns of facial expressions among patients diagnosed with myocardial infarction.

INTERVENTION

On admission to the ED, patients were videotaped during physical examination. Videotapes were reviewed to code the facial action units exhibited by the patients. The presence or absence of creatine kinase (CK) enzymes was determined; these results were blinded to the coders until after all facial actions were coded.

RESULTS

With use of the Facial Action Coding System, 4 facial expressions were found to be associated with true myocardial infarction: lowering the brow, pressing the lips, parting the lips, and turning the head left.

CONCLUSION

Additional research with a larger sample of patients presenting with chest pain is needed to validate the findings of this study. However, if these findings are supported, instruction regarding assessment of specific facial expressions in clinical settings may be warranted.

Changing acute pain management to improve patient outcomes: an educational approach

The United States Agency for Health Care Policy and Research (AHCPR) Acute Pain Management Guidelines were written to provide a scientific basis for practice. Educational programs designed to promote use of the guidelines may change practice in community hospitals. This article describes the development and implementation of an education program for nurses, physicians, and pharmacists in six community hospitals. Program content addressing the use of continuous quality improvement (CQI) teams, detailed pain histories, application of algorithms and dose calculation is described; direct and indirect outcome measures are reviewed. Six months after the program, all three experimental sites reported use of the AHCPR Guidelines in practice. Nurses reported that assessment and documentation of patients' duration of pain were perceived to be the most important caregiver behaviors providing benefit to patients: Across all respondents' reports of regularly performed activities, the activity performed by the largest proportion was assessing and documenting pain using a 0-10 rating scale.