Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident identification of bacterial immunopeptides.

TIMSRescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MSRescore.

The high throughput analysis of proteins with mass spectrometry (MS) is highly valuable for understanding human biology, discovering disease biomarkers, identifying therapeutic targets, and exploring pathogen interactions. To achieve these goals, specialized proteomics subfields, including plasma proteomics, immunopeptidomics, and metaproteomics, must tackle specific analytical challenges, such as an increased identification ambiguity compared to routine proteomics experiments. Technical advancements in MS instrumentation can mitigate these issues by acquiring more discerning information at higher sensitivity levels.

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing.

Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights into community phenotypes and the roles individual members play in diverse ecosystems. Although database-dependent search engines are commonly used for peptide identification, they rely on pre-existing protein databases, which can be limiting for complex, poorly characterized microbiomes.

PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.

Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data.

Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair.

Our understanding of the functional heterogeneity of resident versus recruited macrophages in the diseased liver is limited. A population of recruited lipid-associated macrophages (LAMs) has been reported to populate the diseased liver alongside resident Kupffer cells (KCs). However, the precise roles of these distinct macrophage subsets remain elusive.

Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides.

Unipept, a pioneering software tool in metaproteomics, has significantly advanced the analysis of complex ecosystems by facilitating both taxonomic and functional insights from environmental samples. From the onset, Unipept's capabilities focused on tryptic peptides, utilizing the predictability and consistency of trypsin digestion to efficiently construct a protein reference database. However, the evolving landscape of proteomics and emerging fields like immunopeptidomics necessitate a more versatile approach that extends beyond the analysis of tryptic peptides.

PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins.

Recent improvements in methods and instruments used in mass spectrometry have greatly enhanced the detection of protein post-translational modifications (PTMs). On the computational side, the adoption of open modification search strategies now allows for the identification of a wide variety of PTMs, potentially revealing hundreds to thousands of distinct modifications in biological samples. While the observable part of the proteome is continuously growing, the visualization and interpretation of this vast amount of data in a comprehensive fashion is not yet possible.

Sexual function after surgically corrected menstrual outflow obstruction due to congenital anomalies.

Objectives: To enhance evidence-based knowledge about sexual function and the prevalence of sexual dysfunction after surgical therapy for congenital anomalies with menstrual outflow obstruction.

Materials And Methods: In this long-term case-control study, all patients underwent surgical correction of an obstructive Müllerian anomaly between 1980 and 2013. At the start of the case-control study, patients were at least 18 years old and were two years post their initial operation.

A prognostic molecular signature of hepatic steatosis is spatially heterogeneous and dynamic in human liver.

Hepatic steatosis is a central phenotype in multi-system metabolic dysfunction and is increasing in parallel with the obesity pandemic. We use a translational approach integrating clinical phenotyping and outcomes, circulating proteomics, and tissue transcriptomics to identify dynamic, functional biomarkers of hepatic steatosis. Using multi-modality imaging and broad proteomic profiling, we identify proteins implicated in the progression of hepatic steatosis that are largely encoded by genes enriched at the transcriptional level in the human liver.

Vanishing bile duct syndrome: a sequela of temozolomide and levetiracetam-induced cholestatic liver injury.

Temozolomide (TMZ)-levetiracetam (LEV) combination therapy in glioblastoma management is gradually becoming a mainstay treatment given its superior effect compared with TMZ monotherapy. While there have been previous cases of hepatotoxicity, there are no prior reports of vanishing bile duct syndrome (VBDS) associated with TMZ-LEV combination use. This case report details a male in his 50s who had recently completed TMZ and LEV for right frontal lobe glioblastoma.

Vertical root fracture detection with cone-beam computed tomography in Biodentine™ filled teeth.

Purpose: This study aimed to evaluate the accuracy of detecting vertical root fractures in Biodentine™-filled teeth using the Promax 3Dmax cone-beam computed tomography (CBCT) unit compared to periapical radiographs. It tested hypotheses regarding CBCT's diagnostic superiority in non-root-filled and Biodentine™-root-filled maxillary central incisors and assessed the impact of smaller field of view and lower intensity settings on detection accuracy.

Materials And Methods: Extracted maxillary incisors were divided into groups based on fracture status and root filling material, then placed in a Thiel-embalmed skull to simulate clinical conditions.

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.

Understanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build unifying models of gene regulation capturing sequence determinants across steps of gene expression. However, current models, developed primarily for bulk omics data, fail to capture the cellular heterogeneity and dynamic processes revealed by single-cell multi-modal technologies.

Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial.

Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.

Bioinformatics Pipeline for Processing Single-Cell Data.

Single-cell proteomics can offer valuable insights into dynamic cellular interactions, but identifying proteins at this level is challenging due to their low abundance. In this chapter, we present a state-of-the-art bioinformatics pipeline for single-cell proteomics that combines the search engine Sage (via SearchGUI), identification rescoring with MSRescore, quantification through FlashLFQ, and differential expression analysis using MSqRob2. MSRescore leverages LC-MS/MS behavior predictors, such as MSPIP and DeepLC, to recalibrate scores with Percolator or mokapot.

In Situ Assessment of Uplink Duty Cycles for 4G and 5G Wireless Communications.

In this presented study, we measured in situ the uplink duty cycles of a smartphone for 5G NR and 4G LTE for a total of six use cases covering voice, video, and data applications. The duty cycles were assessed at ten positions near a 4G and 5G base-station site in Belgium. For Twitch, VoLTE, and WhatsApp, the duty cycles ranged between 4% and 22% in time, both for 4G and 5G.

Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links.

In protein-RNA cross-linking mass spectrometry, UV or chemical cross-linking introduces stable bonds between amino acids and nucleic acids in protein-RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA-protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross-linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space.

Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling.

The use of collision cross section (CCS) values derived from ion mobility studies is proving to be an increasingly important tool in the characterization and identification of molecules detected in complex mixtures. Here, a novel machine learning (ML) based method for predicting CCS integrating both molecular modeling (MM) and ML methodologies has been devised and shown to be able to accurately predict CCS values for singly charged small molecular weight molecules from a broad range of chemical classes. The model performed favorably compared to existing models, improving compound identifications for isobaric analytes in terms of ranking and assigning identification probability values to the annotation.

Two-year clinical and radiographic evaluation of ACTIVA BioACTIVE versus Compomer (Dyract® eXtra) in the restoration of class-2 cavities of primary molars: a non-inferior split-mouth randomised clinical trial.

Objectives: The trial aimed to compare the clinical performance and radiographic success of ACTIVA BioACTIVE versus Compomer in restoring class-II cavities of primary molars.

Materials And Methods: A non-inferior split-mouth design was considered. A pre-calculated sample size of 96 molars (48 per group) with class-2 cavities of twenty-one children whose ages ranged from 5 to 10 years were randomly included in the trial.

Association among childhood adversity and susceptibility to interference during varying salience: two studies in healthy males.

Childhood adversity, a prevalent experience, is related to a higher risk for externalizing and internalizing psychopathology. Alterations in the development of cognitive processes, for example in the attention-interference domain may link childhood adversity and psychopathology. Interfering stimuli can vary in their salience, i.

MSRescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0.

Rescoring of peptide-spectrum matches (PSMs) has emerged as a standard procedure for the analysis of tandem mass spectrometry data. This emphasizes the need for software maintenance and continuous improvement for such algorithms. We introduce MSRescore 3.