Christian Panse
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View article: A combination of phenotypic responses and genetic adaptations enables <i>Staphylococcus aureus</i> to withstand inhibitory molecules secreted by <i>Pseudomonas aeruginosa</i>
A combination of phenotypic responses and genetic adaptations enables <i>Staphylococcus aureus</i> to withstand inhibitory molecules secreted by <i>Pseudomonas aeruginosa</i> Open
Staphylococcus aureus and Pseudomonas aeruginosa frequently co-occur in infections, and there is evidence that their interactions can negatively affect disease outcomes. P. aeruginosa is known to be dominant, often compromising S. aureus t…
View article: A combination of phenotypic responses and genetic adaptations enables <i>Staphylococcus aureus</i> to withstand inhibitory molecules secreted by <i>Pseudomonas aeruginosa</i>
A combination of phenotypic responses and genetic adaptations enables <i>Staphylococcus aureus</i> to withstand inhibitory molecules secreted by <i>Pseudomonas aeruginosa</i> Open
Staphylococcus aureus and Pseudomonas aeruginosa frequently co-occur in infections, and there is evidence that their interactions can negatively affect disease outcomes. P. aeruginosa is known to be dominant, often compromising S. aureus t…
View article: <i>prolfquapp</i> ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics
<i>prolfquapp</i> ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics Open
Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. As experiments grow in complexity, involving more samples, groups, and identifi…
View article: A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities
A Multiyear Longitudinal Harmonization Study of Quality Controls in Mass Spectrometry Proteomics Core Facilities Open
Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratorie…
View article: <i>prolfquapp</i>- A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics
<i>prolfquapp</i>- A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics Open
Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis ( DEA ) of proteins. As experiments grow in complexity, involving more samples, groups, and identi…
View article: International symposium on integrative bioinformatics 2024 – editorial
International symposium on integrative bioinformatics 2024 – editorial Open
Integrative Bioinformatics faces the challenge of integrating, aligning, modelling, and simulating data in a coherent fashion to gain deeper insights into complex biological systems. This special issue of the Journal of Integrative Bioinfo…
View article: Koina: Democratizing machine learning for proteomics research
Koina: Democratizing machine learning for proteomics research Open
Recent developments in machine-learning (ML) and deep-learning (DL) have immense potential for applications in proteomics, such as generating spectral libraries, improving peptide identification, and optimizing targeted acquisition modes. …
View article: A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities
A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities Open
Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratorie…
View article: Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences
Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences Open
Core facilities have to offer technologies that best serve the needs of their users and provide them a competitive advantage in research. They have to set up and maintain instruments in the range of ten to a hundred, which produce large am…
View article: prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis
prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis Open
Mass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. Nevertheless, there is a need for a flexible and easy-to-use application programming i…
View article: Quality standards in proteomics research facilities
Quality standards in proteomics research facilities Open
Proteomics research infrastructures and core facilities within the Core for Life alliance advocate for community policies for quality control to ensure high standards in proteomics services.
View article: The rawrr R Package: Direct Access to Orbitrap Data and Beyond
The rawrr R Package: Direct Access to Orbitrap Data and Beyond Open
The Bioconductor project (Nat. Methods2015, 12 (2), 115-121) has shown that the R statistical environment is a highly valuable tool for genomics data analysis, but with respect to proteomics, we are still missing low-level infrastructure t…
View article: rawR - Direct access to raw mass spectrometry data in R
rawR - Direct access to raw mass spectrometry data in R Open
The Bioconductor project has shown that the R statistical environment is a highly valuable tool for genomics data analysis 1 , but with respect to proteomics we are still missing low level infrastructure to enable performant and robust ana…
View article: Ultraviolet Photodissociation for Non-Target Screening-Based Identification of Organic Micro-Pollutants in Water Samples
Ultraviolet Photodissociation for Non-Target Screening-Based Identification of Organic Micro-Pollutants in Water Samples Open
Non-target screening (NTS) based on the combination of liquid chromatography coupled to high-resolution mass spectrometry has become the key method to identify organic micro-pollutants (OMPs) in water samples. However, a large number of co…
View article: Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison
Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison Open
Here we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison ( https://www.proteomicsdb.org/use/ ). Mass spectra under investigation can either be …
View article: Ultraviolet photodissociation for non-target screening based identification of organic micro-pollutants in water samples
Ultraviolet photodissociation for non-target screening based identification of organic micro-pollutants in water samples Open
Raw LC-HRMS data that was used for demonstrating the the use of the fragmentation technique ultraviolet photodissociation (UVPD) for the structural elucidation of organic micropollutants (OMPs) in water samples in combination with the 'uvp…
View article: Ultraviolet photodissociation for non-target screening based identification of organic micro-pollutants in water samples
Ultraviolet photodissociation for non-target screening based identification of organic micro-pollutants in water samples Open
Raw LC-HRMS data that was used for demonstrating the the use of the fragmentation technique ultraviolet photodissociation (UVPD) for the structural elucidation of organic micropollutants (OMPs) in water samples in combination with the 'uvp…
View article: <tt>rawDiag</tt> - an R package supporting rational LC-MS method optimization for bottom-up proteomics
rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics Open
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) is a non-trivial task. Here we present rawDiag , a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots o…
View article: Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles
Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles Open
Binding protein generation relies on laborious screening cascades that process candidate molecules individually. To break with this paradigm, we developed NestLink, a binder selection and identification technology able to biophysically cha…
View article: Total lipid, phospholipid and cholesterol contents of six marine shrimps of Mumbai, Maharashtra
Total lipid, phospholipid and cholesterol contents of six marine shrimps of Mumbai, Maharashtra Open
The total lipid, phospholipids and cholesterol contents in the muscles of six marine shrimps viz., Parapenaeopsis stylifera, Parapenaeopsis sculptilis, Metapenaeus brevicornis, Litopenaeus vannamei, Nematopalaemon tenuipes and Acetes indic…