Rescuing error control in crosslinking mass spectrometry

Crosslinking mass spectrometry is a powerful tool to study protein-protein interactions under native or near-native conditions in complex mixtures. Through novel search controls, we show how biassing results towards likely correct proteins can subtly undermine error estimation of crosslinks, with significant consequences. Without adjustments to address this issue, we have misidentified an average of 260 interspecies protein-protein interactions across 16 analyses in which we synthetically mixed data of different species, misleadingly suggesting profound biological connections that do not exist. We also demonstrate how data analysis procedures can be tested and refined to restore the integrity of the decoy-false positive relationship, a crucial element for reliably identifying protein-protein interactions.</p

Nop9 is an RNA binding protein present in pre-40S ribosomes and required for 18S rRNA synthesis in yeast

Proteomic analyses in yeast have identified a large number of proteins that are associated with preribosomal particles. However, the product of the yeast ORF YJL010C, herein designated as Nop9, failed to be identified in any previous physical or genetic analysis of preribosomes. Here we report that Nop9 is a nucleolar protein, which is associated with 90S and 40S preribosomes. In cells depleted of Nop9p, early cleavages of the 35S pre-rRNA are inhibited, resulting in the nucleolar retention of accumulated precursors and a failure to synthesize 18S rRNA. Nop9 contains multiple pumilio-like putative RNA binding repeats and displays robust in vitro RNA binding activity. The identification of Nop9p as a novel, essential factor in the nuclear maturation of 90S and pre-40S ribosomal subunits shows that the complement of ribosome synthesis factors remains incomplete

From student to expert in a week

It can be challenging to effectively impart higher education content to students. We experienced such difficulty in a lecture series with invited senior scientists presenting their area of Biotech research. Instead of a vivid exchange with the expert, we observed limited and restrained student contributions. In qualitative interviews with these students we learned that they perceive their knowledge disparity as too big and the fear of being embarrassed by asking “stupid” questions obstructed their participation. This let us to radically rethink the course design resulting in our own interpretation of flipped classroom, peer learning and student empowerment. We designed an engineering course that focuses on providing master students with the best possible environment to gain theoretical knowledge in a new field within a limited time period (currently: six weeks - six topics) aiming to empower them in these topics by acquiring new knowledge on their own. Based on seed questions and tag words, students conduct background research and create a team presentation for an invited field expert, thereby getting prepared for a subsequent indepth discussion with the expert. The current layout is the product of an iterative process over the course of five years, and several rounds of fine-tuning within each year, based on extensive student and instructor feedback. Students particularly appreciate the positive in-course atmosphere with a focus on growth-mindset, the strong experience in teamwork, being taken seriously, and making contact with field experts and frontiers of current knowledge

Departmental seminar series and journal club with enhanced learning outcomes

Listening to scientific presentations and reading scientific literature are core activities of any scientist, and frequent components of students' curricula. When employing these activities in teaching, finding the right balance between student instruction and autonomous learning is important for best learning outcomes and teachers’ workload. We here present our course design for a coordinated lecture series and journal club, that finds this balance by leveraging modern learning concepts in a digital environment. Participating students were tasked to read a landmark scientific paper every week ahead of a lecture by a scientist with practical experience on the topic of that paper, often an author of that week’s paper. Students then had to hand in written answers to three questions probing their understanding of the topic and the paper. In a subsequent seminar, activating questions were discussed by the students in break-out rooms and then answered by randomly chosen students in class, followed by a broad discussion that included the homework questions. Students gave weekly feedback on their learning progress and experience, and the course was then dynamically adapted accordingly. This yielded a course with largely increased course capacity, reduced teachers’ workload, and substantially enhanced learning outcomes, qualitatively and quantitatively compared to previous implementations of the course

Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues

Hydrophilic strong anion exchange chromatography (hSAX) is becoming a popular method for the prefractionation of proteomic samples. However, the use and further development of this approach is affected by the limited understanding of its retention mechanism and the absence of elution time prediction. Using a set of 59 297 confidentially identified peptides, we performed an explorative analysis and built a predictive deep learning model. As expected, charged residues are the major contributors to the retention time through electrostatic interactions. Aspartic acid and glutamic acid have a strong retaining effect and lysine and arginine have a strong repulsion effect. In addition, we also find the involvement of aromatic amino acids. This suggests a substantial contribution of cation−π interactions to the retention mechanism. The deep learning approach was validated using 5-fold cross-validation (CV) yielding a mean prediction accuracy of 70% during CV and 68% on a hold-out validation set. The results of this study emphasize that not only electrostatic interactions but rather diverse types of interactions must be integrated to build a reliable hSAX retention time predictor

Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow

The European Proteomics Association (EuPA) 2012 Scientific Congress ‘New Horizons and Applications for Proteomics’, hosted by the British Society for Proteome Research (BSPR) Glasgow, Scotland, UK, 12 July 2012 Cross-linking/mass spectrometry ended decades of method developments and entered the era of applications at this year’s European Proteomics Association meeting. The train has started moving, with successful applications of this tool by multiple pioneering laboratories addressing biological and structural problems. Proteomics, on the other side, sees ever increasing data volumes, leading to questions as to how to store the data mountain publically, use it and convert it into testable hypotheses. The European Proteomics Association meeting has been complementary to the American Society for Mass Spectrometry meeting in many ways, also thanks to its more manageable size and the vision of the organizers in inviting some of Europe’s best emerging minds