Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination.

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence.

Post-traumatic reaction of Israeli Jewish and Arab children exposed to rocket attacks before and after teacher-delivered intervention.

BACKGROUND: Belonging to ethnic minorities is a risk factor for traumatized children. this study investigated the influence of exposure to rocket attacks during the 2006 Lebanon War on Jewish and two groups of arab Israeli students and the effect of implementing a teacher-delivered intervention focusing on resilience enhancement. METHOD: Children from both ethnic groups (N = 1,372) were assessed for stressful life events, symptoms and parental concern regarding adaptation before the 16- week program (t1) and after its completion (t2). RESULTS: arab children reported more severe symptoms at t1. the three groups showed a significant decrease to the same level at t2. Both ethnic groups differed in the level of parental concern and in the way stressful life events affected children's symptoms. CONCLUSIONS: the results suggest that school-based programs with teachers as clinical mediators could be a valuable, cost-effective cross-cultural model of intervention after mass trauma, moderating vulnerabilities of ethnic minorities.