The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF.

Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.

Ex vivo optical coherence tomography combined with near infrared targeted fluorescence: towards esophageal cancer detection.

Early detection of (pre)malignant esophageal lesions is critical to improve esophageal cancer morbidity and mortality rates. In patients with advanced esophageal adenocarcinoma (EAC) who undergo neoadjuvant chemoradiation therapy, the efficacy of therapy could be optimized and unnecessary surgery prevented by the reliable assessment of residual tumors after therapy. Optical coherence tomography (OCT) provides structural images at a (sub)-cellular level and has the potential to visualize morphological changes in tissue.

Proceedings of the EuBIC-MS developers meeting 2023.

The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verità in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on "Artificial Intelligence in proteomics" to stimulate future directions in the MS-driven omics areas.

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.

Performance Assessment and Quality Control of Fluorescence Molecular Endoscopy With a Multi-Parametric Rigid Standard.

Fluorescence molecular endoscopy (FME) is emerging as a "red-flag" technique with potential to deliver earlier, faster, and more personalized detection of disease in the gastrointestinal tract, including cancer, and to gain insights into novel drug distribution, dose finding, and response prediction. However, to date, the performance of FME systems is assessed mainly by endoscopists during a procedure, leading to arbitrary, potentially biased, and heavily subjective assessment. This approach significantly affects the repeatability of the procedures and the interpretation or comparison of the acquired data, representing a major bottleneck towards the clinical translation of the technology.

Occupational Therapy Using Zones of Regulation™ Concepts: A Feasibility Study.

There is a lack of peer-reviewed research on occupational therapy using Zones of Regulation™ concepts for autistic youth. The purpose of this article is to describe the feasibility of a newly-developed occupational therapy intervention using Zones of Regulation™ concepts (OT-ZOR) for autistic youth. Specifically, we aimed to evaluate: (a) participant recruitment, retention, and attendance; (b) intervention fidelity, safety, and assessment completion; (c) intervention acceptability; and (d) preliminary participant outcomes.

Fluorescently labelled vedolizumab to visualise drug distribution and mucosal target cells in inflammatory bowel disease.

Objective: Improving patient selection and development of biological therapies such as vedolizumab in IBD requires a thorough understanding of the mechanism of action and target binding, thereby providing individualised treatment strategies. We aimed to visualise the macroscopic and microscopic distribution of intravenous injected fluorescently labelled vedolizumab, vedo-800CW, and identify its target cells using fluorescence molecular imaging (FMI).

Design: Forty three FMI procedures were performed, which consisted of macroscopic in vivo assessment during endoscopy, followed by macroscopic and microscopic ex vivo imaging.

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.

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MSRescore with MSPIP timsTOF fragmentation prediction model.

Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS).

The potential usefulness of standardized assessments to measure participant outcomes of adaptive/therapeutic horseback riding: a survey study.

Adaptive or therapeutic riding (A/TR) is a recreational activity which provides mounted and ground-based horsemanship opportunities adapted to the abilities of the participants. A/TR provides physical and psychological benefits to participants with diverse disabilities, including physical, developmental, cognitive, and age-related disabilities, promoting higher quality of life. A/TR professionals may be limited in their capacity to implement outcome assessments and report the benefits of their community-based A/TR services to a broad audience.

The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions.

Background: It is increasingly recognized that conventional food production systems are not able to meet the globally increasing protein needs, resulting in overexploitation and depletion of resources, and environmental degradation. In this context, microbial biomass has emerged as a promising sustainable protein alternative. Nevertheless, often no consideration is given on the fact that the cultivation conditions affect the composition of microbial cells, and hence their quality and nutritional value.

Updated MS²PIP web server supports cutting-edge proteomics applications.

Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such as immunopeptidomics and the full-proteome identification of data independent acquisition spectra. Since its inception, the MS²PIP peptide spectrum predictor has been widely used for various downstream applications, mostly thanks to its accuracy, ease-of-use, and broad applicability. We here present a thoroughly updated version of the MS²PIP web server, which includes new and more performant prediction models for both tryptic- and non-tryptic peptides, for immunopeptides, and for CID-fragmented TMT-labeled peptides.

ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics.

Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the high levels of data reduction that occur between raw data and machine learning-ready data. Since predictive proteomics is an emerging field, when predicting peptide behavior in LC-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility.

Quality Control for the Target Decoy Approach for Peptide Identification.

Reliable peptide identification is key in mass spectrometry (MS) based proteomics. To this end, the target decoy approach (TDA) has become the cornerstone for extracting a set of reliable peptide-to-spectrum matches (PSMs) that will be used in downstream analysis. Indeed, TDA is now the default method to estimate the false discovery rate (FDR) for a given set of PSMs, and users typically view it as a universal solution for assessing the FDR in the peptide identification step.

Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete.

Detection of Early Esophageal Neoplastic Barrett Lesions with Quantified Fluorescence Molecular Endoscopy Using Cetuximab-800CW.

Esophageal adenocarcinoma causes 6% of cancer-related deaths worldwide. Near-infrared fluorescence molecular endoscopy (NIR-FME) uses a tracer that targets overexpressed proteins. In this study, we aimed to investigate the feasibility of an epidermal growth factor receptor (EGFR)-targeted tracer, cetuximab-800CW, to improve detection of early-stage esophageal adenocarcinoma.

psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results.

A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist to solve this problem, these are far from universally supported by search engines.

CovMS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein.

The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The CovMS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma and has increased sensitivity into the attomole range, a 1000-fold improvement compared to direct detection in a matrix.

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes.

Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens.

Mucosal Eosinophil Abundance in Non-Inflamed Colonic Tissue Is Associated with Response to Vedolizumab Induction Therapy in Inflammatory Bowel Disease.

Vedolizumab is used as a treatment for patients with inflammatory bowel disease (IBD), but induction therapy leads to clinical response and remission in approximately 55% and 30% of patients with IBD, respectively. In this study, we aimed to explore the predictive value of mucosal eosinophils and serum eotaxin-1 regarding response to vedolizumab induction therapy. Eighty-four (84) patients with IBD (37 Crohn’s disease [CD], 47 ulcerative colitis [UC]) were included.

Self-Regulation Mediates Therapeutic Horseback Riding Social Functioning Outcomes in Youth With Autism Spectrum Disorder.

Emerging evidence suggests therapeutic horseback riding improves self-regulation behaviors, social functioning, and language in youth with autism spectrum disorder (ASD). It has been theorized that interacting with horses is calming for youth with ASD, which may influence social and language outcomes. The current study is an exploratory secondary mediation analysis of a previously published randomized controlled trial of therapeutic horseback riding for youth with ASD.

Today's Mistakes and Tomorrow's Wisdom in Endoscopic Imaging of Barrett's Esophagus.

Background: Esophageal adenocarcinoma (EAC) is one of the main causes of cancer-related deaths worldwide and its incidence is rising. Barrett's esophagus (BE) can develop low- and high-grade dysplasia which can progress to EAC overtime. The golden standard to detect dysplastic BE (DBE) or EAC is surveillance with high-definition white-light endoscopy (HD-WLE) and random biopsies according to the Seattle protocol.

MSRescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.

Immunopeptidomics aims to identify major histocompatibility complex (MHC)-presented peptides on almost all cells that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the nontryptic nature of immunopeptides, complicating their identification. Previously, peak intensity predictions by MSPIP and retention time predictions by DeepLC have been shown to improve tryptic peptide identifications when rescoring peptide-spectrum matches with Percolator.