HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases. Commonly used protein databases contain a minimal level of redundancy, and thus, are not suitable data sources for searching polymorphic T cell epitopes, either in normal or ARFs. At the same time, however, these databases contain much non-polymorphic sequence information, thereby complicating the matching of recorded and theoretical spectra, and increasing the potential for finding false positives. Therefore, we created a database with peptides from ARFs and peptide variation arising from single nucleotide polymorphisms (SNPs). It is based on the human mRNA sequences from the well-annotated reference sequence (RefSeq) database and associated variation information derived from the Single Nucleotide Polymorphism Database (dbSNP). In this process, we removed all non-polymorphic information. Investigation of the frequency of SNPs in the dbSNP revealed that many SNPs are non-polymorphic “SNPs”. Therefore, we removed those from our dedicated database, and this resulted in a comprehensive high quality database, which we coined the Human Short Peptide Variation Database (HSPVdb). The value of our HSPVdb is shown by identification of the majority of published polymorphic SNP- and/or ARF-derived epitopes from a mass spectrometry-based proteomics workflow, and by a large variety of polymorphic peptides identified as potential T cell epitopes in the HLA-ligandome presented by the Epstein–Barr virus cells

Drinking Motives Mediate the Relationship Between Facets of Mindfulness and Problematic Alcohol Use

Mindfulness is a multi-faceted construct, and research suggests that certain components (e.g., Acting with Awareness, Nonjudging) are associated with less problematic alcohol use. Recent research has examined whether specific drinking motives mediate the relationship between facets of mindfulness and alcohol use. The current study sought to extend this research by examining whether certain drinking motives would mediate the relationship between facets of mindfulness and problematic alcohol use in a sample of 207 college students classified as engaging in problematic drinking. Participants completed the Five Facet Mindfulness Questionnaire (FFMQ), Drinking Motives Questionnaire-Revised (DMQ-R), and Alcohol Use Disorders Identification Test (AUDIT). Results indicated that lower levels of Coping motives significantly mediated the relationship between greater Acting with Awareness and lower AUDIT score and between greater Nonjudging and lower AUDIT score. Lower levels of Conformity motives significantly mediated the relationship between greater Acting with Awareness and lower AUDIT score. These findings offer insight into specific mechanisms through which mindfulness is linked to less problematic drinking, and also highlight associations among mindfulness, drinking motives, and alcohol use among a sample of problematic college student drinkers. Future research should determine whether interventions that emphasize Acting with Awareness and Nonjudging facets of mindfulness and/or target coping and conformity motives could be effective for reducing problematic drinking in college students