FG Bioanalytik

22 Items

Recent Submissions
Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry

Giese, Sven H. ; Sinn, Ludwig R. ; Wegner, Fritz ; Rappsilber, Juri (2021-05-28)

Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits the numbers of protein–protein interactions that can be confidently identified. Here, we leverage chromatographic retention time information to aid ...

Peptide retention in hydrophilic strong anion exchange chromatography is driven by charged and aromatic residues

Giese, Sven H. ; Ishihama, Yasushi ; Rappsilber, Juri (2018-03-12)

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 ...

Noncovalently associated peptides observed during liquid chromatography-mass spectrometry and their effect on cross-link analyses

Giese, Sven H. ; Belsom, Adam ; Sinn, Ludwig ; Fischer, Lutz ; Rappsilber, Juri (2019-01-16)

Cross-linking mass spectrometry draws structural information from covalently linked peptide pairs. When these links do not match to previous structural models, they may indicate changes in protein conformation. Unfortunately, such links can also be the result of experimental error or artifacts. Here, we describe the observation of noncovalently associated peptides during liquid chromatography-m...

Optimized fragmentation regime for diazirine photo-cross-linked peptides

Giese, Sven H. ; Belsom, Adam ; Rappsilber, Juri (2016-07-25)

Cross-linking/mass spectrometry has evolved into a robust technology that reveals structural insights into proteins and protein complexes. We leverage a new tribrid instrument with improved fragmentation capacities in a systematic comparison to identify which fragmentation method would be best for the identification of cross-linked peptides. Specifically, we explored three fragmentation methods...

A study into the Collision-induced Dissociation (CID) behavior of cross-linked peptides

Giese, Sven H. ; Fischer, Lutz ; Rappsilber, Juri (2016-03-01)

Cross-linking/mass spectrometry resolves protein–protein interactions or protein folds by help of distance constraints. Cross-linkers with specific properties such as isotope-labeled or collision-induced dissociation (CID)- cleavable cross-linkers are in frequent use to simplify the identification of cross-linked peptides. Here, we analyzed the mass spectrometric behavior of 910 unique crosslin...

Antiinflammatory Medicinal Plants from the Ugandan Greater Mpigi Region Act as Potent Inhibitors in the COX-2/PGH2 Pathway

Schultz, Fabien ; Osuji, Ogechi Favour ; Wack, Barbara ; Anywar, Godwin ; Garbe, Leif-Alexander (2021-02-12)

Our study investigates 16 medicinal plants via assessment of inhibition of proinflammatory enzymes such as cyclooxygenases (COX). The plants are used by traditional healers in the Greater Mpigi region in Uganda to treat inflammation and related disorders. We present results of diverse in vitro experiments performed with 76 different plant extracts, namely, (1) selective COX-2 and COX-1 inhibito...

Rationally designed synthesis of bright AgInS2/ZnS quantum dots with emission control

Soares, José X. ; Wegner, K. David ; Ribeiro, David S. M. ; Melo, Armindo ; Häusler, Ines ; Santos, João L. M. ; Resch-Genger, Ute (2020-06-19)

In the blossoming field of Cd-free semiconductor quantum dots (QDs), ternary I-III-VI QDs have received increasing attention due to the ease of the environmentally friendly synthesis of high-quality materials in water, their high photoluminescence (PL) quantum yields (QYs) in the red and near infrared (NIR) region, and their inherently low toxicity. Moreover, their oxygen-insensitive long PL li...

A primer on data analytics in functional genomics: How to move from data to insight?

Grabowski, Piotr ; Rappsilber, Juri (2018-12-03)

High-throughput technologies are now widely used in the life sciences field and are producing ever-increasing amounts and diversity of data. While many laboratories and even undergraduate students generate high-throughput data, analyzing these results requires a skill set that is traditionally reserved for bioinformaticians. Learning to program using languages such as R and Python and making ...

Epigenetic variability confounds transcriptome but not proteome profiling for coexpression-based gene function prediction

Grabowski, Piotr ; Kustatscher, Georg ; Rappsilber, Juri (2018-07-24)

Genes are often coexpressed with their genomic neighbors, even if these are functionally unrelated. For small expression changes driven by genetic variation within the same cell type, non-functional mRNA coexpression is not propagated to the protein level. However, it is unclear if protein levels are also buffered against any non-functional mRNA coexpression accompanying large, regulated change...

Pervasive coexpression of spatially proximal genes is buffered at the protein level

Kustatscher, Georg ; Grabowski, Piotr ; Rappsilber, Juri (2017-08-23)

Genes are not randomly distributed in the genome. In humans, 10% of protein‐coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level...

Machine learning on protein expression data

Grabowski, Piotr (2020)

Integrating gene expression data at transcript and protein level from many experiments helps in understanding functional relationships between genes, transcripts and the proteins they encode. Such approaches, collectively known as co-expression analysis, use various statistical methods to create pairwise association scores between genes or proteins. Co-expression analyses have been traditionall...

Chemische Synthese von isotopenmarkierten Standards zur Analyse von unerwünschten Substanzen (NIAS) aus Lebensmittelkontaktmaterialien

Manowski, Aneta Grazyna (2019)

Eins der Hauptziele dieser Arbeit ist die Synthese von neuen Referenzsubstanzen für nicht absichtlich hinzugefügte Substanzen (NIAS) aus Polymeren, die in Lebensmittelkontaktmaterialien Einsatz finden, dem Epoxidharz und dem Polyamid-6. Durch Einsatz von Schutzgruppenstrategien konnten vier neue oligomere Referenzsubstanzen von Bisphenol A (BPA) erfolgreich synthetisiert werden: BADGE∙BPA, BADG...

G9a/GLP complex maintains imprinted DNA methylation in embryonic stem cells

Zhang, Tuo ; Termanis, Ausma ; Özkan, Burak ; Bao, Xun X. ; Culley, Jayne ; de Lima Alves, Flavia ; Rappsilber, Juri ; Ramsahoye, Bernard ; Stancheva, Irina (2016-03-24)

DNA methylation at imprinting control regions (ICRs) is established in gametes in a sex-specific manner and has to be stably maintained during development and in somatic cells to ensure the correct monoallelic expression of imprinted genes. In addition to DNA methylation, the ICRs are marked by allele-specific histone modifications. Whether these marks are essential for maintenance of genomic i...

Kicking against the PRCs

Liang, Shih Chieh ; Hartwig, Ben ; Perera, Pumi ; Mora-García, Santiago ; Leau, Erica de ; Thornton, Harry ; Lima Alves, Flavia de ; Rappsilber, Juri ; Yang, Suxin ; James, Geo Velikkakam ; Schneeberger, Korbinian ; Finnegan, E. Jean ; Turck, Franziska ; Goodrich, Justin (2015)

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and conseq...

A single α helix drives extensive remodeling of the proteasome lid and completion of regulatory particle assembly

Tomko, Robert J. ; Taylor, David W. ; Chen, Zhuo A. ; Wang, Hong-Wei ; Rappsilber, Juri ; Hochstrasser, Mark (2015)

Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis culminates with the joining of two large subcomplexes, the lid and base. In yeast and mammals, the lid appears to assemble completely before attaching to the base, but how this hierarchical assembly is en...

Functional inhibition of acid sphingomyelinase by Fluphenazine triggers hypoxia-specific tumor cell death

Klutzny, Saskia ; Lesche, Ralf ; Keck, Matthias ; Kaulfuss, Stefan ; Schlicker, Andreas ; Christian, Sven ; Sperl, Carolyn ; Neuhaus, Roland ; Mowat, Jeffrey ; Steckel, Michael ; Riefke, Björn ; Prechtl, Stefan ; Parczyk, Karsten ; Steigemann, Patrick (2017)

Owing to lagging or insufficient neo-angiogenesis, hypoxia is a feature of most solid tumors. Hypoxic tumor regions contribute to resistance against antiproliferative chemotherapeutics, radiotherapy and immunotherapy. Targeting cells in hypoxic tumor areas is therefore an important strategy for cancer treatment. Most approaches for targeting hypoxic cells focus on the inhibition of hypoxia adap...

Elucidation of orthopoxvirus adaptation mechanisms by proteomics and genomics

Grossegesse, Marica (2018)

Adaptive changes of viruses enable the virus-host coevolution and infection of new host species. While viruses with an RNA genome adapt primarily by genomic variabilities, adaptation mechanisms of viruses with a DNA genome have remained largely elusive. Since genomes of DNA viruses are more stable compared to genomes of RNA viruses, it is assumed that mechanisms other than genomic changes under...

Proteomics of a fuzzy organelle: interphase chromatin

Kustatscher, Georg ; Hégarat, Nadia ; Wills, Karen L. H. ; Furlan, Cristina ; Bukowski-Wills, Jimi-Carlo ; Hochegger, Helfrid ; Rappsilber, Juri (2014)

Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and canno...

Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11

Schneider, Michael ; Belsom, Adam ; Rappsilber, Juri ; Brock, Oliver (2016)

Hybrid approaches combine computational methods with experimental data. The information contained in the experimental data can be leveraged to probe the structure of proteins otherwise elusive to computational methods. Compared with computational methods, the structures produced by hybrid methods exhibit some degree of experimental validation. In spite of these advantages, most hybrid methods h...

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data

Kustatscher, Georg ; Grabowski, Piotr ; Rappsilber, Juri (2016)

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a ...