A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline.

Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.

Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.

Targeted mass spectrometry (MS) methods are powerful tools for selective and sensitive analysis of peptides identified by global discovery experiments. Selected reaction monitoring (SRM) is currently the most widely accepted MS method in the clinic, due to its reliability and analytical performance. However, due to limited throughput and the difficulty in setting up and analyzing large scale assays, SRM and parallel reaction monitoring (PRM) are typically used only for very refined assays of on the order of 100 targets or less. Here we introduce a new MS platform with a quadrupole mass filter, collision cell, linear ion trap architecture that has increased acquisition rates compared to the analogous hardware found in the Orbitrap™ Tribrid™ series instruments. The platform can target more analytes than existing SRM and PRM instruments - in the range of 5000 to 8000 peptides per hour. This capability for high multiplexing is enabled by acquisition rates of 70-100 Hz for peptide applications, and the incorporation of real-time chromatogram alignment that adjusts for retention time drift and enables narrow time scheduled acquisition windows. Finally, we describe a Skyline external software tool that implements the building of targeted methods based on data independent acquisition chromatogram libraries or unscheduled analysis of heavy labeled standards. We show that the platform delivers ~10x lower LOQs than traditional SRM analysis for a highly multiplex assay and also demonstrate how analytical figures of merit change while varying method duration with a constant number of analytes, or by keeping a constant time duration while varying the number of analytes.

Amniotic fluid embolism: 20-year incidence and case-fatality trends in the United States.

OBJECTIVE: To estimate incidence and case-fatality rates of amniotic fluid embolism (AFE) and to examine their temporal trends. STUDY DESIGN: Population-based retrospective cohort study using the 2000-2019 Health Care Cost and Utilization Project, Nationwide Inpatient Sample (HCUP-NIS). Annual population rates were estimated using HCUP-NIS specific weighting. Descriptive analyses and logistic regression described trends within the cohort. RESULTS: Over the study period, AFE incidence rate remained stable (mean 4.9 cases/100,000 deliveries) and the case-fatality rate declined (mean 17.7 %,95 % CI 16.40-10.09). Highest AFE incidence rates and fatality rates were in women ≥ 35 years, African-Americans, and in urban-teaching hospitals. AFE mortality rates decreased among Hispanics. CONCLUSION: AFE rates remained stable and fatality rates declined over time. Highest rates of AFE occurrence and death were in women who typically have greater risk of experiencing adverse obstetrical outcomes. Continued research into early diagnostic methods and effective treatments are needed to further improve AFE incidence and mortality rates.

Neonatal outcomes of planned vaginal delivery versus planned cesarean section for breech presentation at term: Population-based study on 546,842 breech births across the United States between 2008 and 2017.

INTRODUCTION: Over the last several decades, cesarean delivery has been recommended as the safest mode of delivery for breech presentations. The purpose of this study was to evaluate the outcomes of planned vaginal births with planned cesarean births in breech presenting fetuses. METHODS: This retrospective population-based cohort study utilized data from the United States' Period Linked Birth-Infant Death Public Use Files from 2008 to 2017. All term singleton breech deliveries of a live baby without congenital anomalies were identified (n = 546,842) and divided into two cohorts: women who had a planned vaginal birth (n = 116,828), and women who had a planned cesarean section (n = 430,014). Multivariate logistic regression models, adjusted for maternal baseline characteristics, examined the associations between the planned delivery method and neonatal outcomes. RESULTS: It was observed that 26.14 % of the planned vaginal birth cohort had a vaginal delivery. In adjusted analyses, undergoing a planned vaginal birth for breech delivery was associated with an increased risk of adverse neonatal outcomes including infant death, OR 1.32, 95 % CI 1.16-1.52, admission to NICU,1.23, 1.19-1.27, ventilation support at 〈 6 h of life, 1.47, 1.42-1.52, ventilation support at 〉 6 h of life, 1.19, 1.08-1.31, and Apgar score of ≤3 at 5 min, 2.27, 2.06-2.50. CONCLUSION: In women carrying fetuses in breech presentation, having a planned vaginal birth had a low success rate and was associated with increased risk of neonatal morbidity and mortality. Women should be carefully counselled on the risks associated with breech vaginal delivery as well as the low success rate of vaginal delivery.

Obstetrical and neonatal outcomes in women with gestational Lyme disease.

OBJECTIVE: The incidence of Lyme disease (LD) infections has risen in recent decades. Gestational LD has been associated with adverse pregnancy outcomes; however, the results have been contradictory. The study objective was to examine the effects of gestational LD on obstetrical and neonatal outcomes. METHODS: Using the Healthcare Cost & Utilization Project National (Nationwide) Inpatient Sample from the United States, we conducted a retrospective cohort study of pregnant patients admitted to the hospital between 2016 and 2019. The exposed group consisted of pregnant patients with gestational LD infection (International Classification of Diseases, Tenth Revision [ICD-10] code A692x), while the comparison group consisted of pregnant patients without gestational LD. Descriptive statistics and multivariate logistic regression models, adjusted for baseline maternal characteristics, were used to determine the associations between gestational LD and obstetrical and neonatal outcomes. RESULTS: The cohort included 2 943 575 women, 226 of whom were diagnosed with LD during pregnancy. The incidence of LD was 7.67 per 100 000 pregnancy admissions. The incidence of gestational LD was stable over the study period. Pregnant patients with LD were more likely white, older, to have private health insurance, and to belong to a higher income quartile. Gestational LD was associated with an increased risk of placental abruption (adjusted odds ratio [aOR], 3.45 [95% confidence interval (CI), 1.53-7.80]) and preterm birth (aOR, 1.58 [95% CI, 1.03-2.42]). CONCLUSION: Gestational LD is associated with a higher risk of placental abruption and preterm birth. Pregnancies complicated by LD, while associated with a higher risk of certain adverse outcomes, can be followed in most healthcare settings.

Cardiovascular Severe Maternal Morbidity and Mortality at Delivery in the United States: A Population-Based Study.

Background: Cardiovascular conditions are the leading cause of maternal mortality in North America. Objectives: The purpose of this study was to examine the relationship between cardiovascular severe maternal morbidity (CSMM) and mortality during delivery hospitalization. Methods: We performed a cohort study using the Health Care Cost and Utilization Project, Nationwide Inpatient Sample, and identified delivery hospitalizations with CSMM from 1999 to 2015. We described temporal trends in the incidence of CSMM and its associated case-fatality. Among individuals with CSMM, we evaluated the association between participant characteristics and mortality using logistic regression analyses. Results: Of 13,791,605 delivery hospitalizations, 11,152 were complicated by CSMM. Of those, 495 resulted in mortality. The overall incidence of CSMM was 8.09 per 10,000 delivery hospitalizations (95% CI: 7.94-8.24), increasing from 7.76 to 8.38 per 10,000 delivery hospitalizations over 15 years (P < 0.001). The overall case-fatality for CSMM was 4.44 per 100 CSMM (95% CI: 4.06-4.85), decreasing from 6.55 to 2.50 per 100 CSMM events over the study period (P = 0.035). Among participants with CSMM, Black (adjusted odds ratio [aOR]: 1.80; 95% CI: 1.39-2.32) and Hispanic (aOR: 1.44; 95% CI: 1.09-1.90) women and those with Medicaid insurance (aOR: 1.52; 95% CI: 1.22-1.88), postpartum hemorrhage (aOR: 4.06; 95% CI: 3.05-5.41), or systemic lupus erythematosus (aOR: 2.50; 95% CI: 1.31-4.78) were at increased risk of mortality. Conclusions: The incidence of CSMM increased over 15 years, reflecting transformations within the obstetric population. Although it decreased during the study period, case-fatality from CSMM remained elevated. Several factors associated with mortality from CSMM were identified.