Ulrike Kusebauch
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View article: A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS
A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS Open
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori genera…
View article: A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon
A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon Open
While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we col…
View article: Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers
Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers Open
The analysis of protein phosphorylation site identification by mass spectrometry-based methods continues to improve with increased efficiency at multiple points of the pipeline including affinity isolation, sample handling with automated p…
View article: Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers
Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers Open
The analysis of protein phosphorylation site identification by mass spectrometry-based methods continues to improve with increased efficiency at multiple points of the pipeline including affinity isolation, sample handling with automated p…
View article: Supplemental Files — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon
Supplemental Files — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon Open
Supplemental Files S1-S8. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lívia …
View article: Supplemental Tables — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon
Supplemental Tables — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon Open
Supplemental Tables S1-S6. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lívia…
View article: Supplemental Data Sets — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon
Supplemental Data Sets — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon Open
Supplemental Data Sets S1-S8. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lí…
View article: Supplemental Tables — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon
Supplemental Tables — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon Open
Supplemental Tables S1-S6. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lívia…
View article: A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon
A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon Open
The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation on environmental acclimation is underexplored for organisms of the domain Archaea. Here, we have investigated the scale of po…
View article: Long-read DNA-Seq of SmAP1 knockout strains
Long-read DNA-Seq of SmAP1 knockout strains Open
Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 μg/mL) complex medium (CM) until mid-exponential phase (OD600nm = 0.5). The cultures were grown…
View article: Long-read DNA-Seq of SmAP1 knockout strains
Long-read DNA-Seq of SmAP1 knockout strains Open
Halobacterium salinarum knockout strains (delta-Ura3: control; delta-Ura3/delta-SmAP1: SmAP1 knockout) were cultured in uracil-supplemented (50 μg/mL) complex medium (CM) until mid-exponential phase (OD600nm = 0.5). The cultures were grown…
View article: Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age
Systems-level patterns in biological processes are changed under prolongevity interventions and across biological age Open
Aging manifests as progressive deterioration in cellular and systemic homeostasis, requiring systems-level perspectives to understand the gradual molecular dysregulation of underlying biological processes. Here, we report systems-level cha…
View article: Engineered SH2 Domains for Targeted Phosphoproteomics
Engineered SH2 Domains for Targeted Phosphoproteomics Open
A comprehensive analysis of the phosphoproteome is essential for understanding molecular mechanisms of human diseases. However, current tools used to enrich phosphotyrosine (pTyr) are limited in their applicability and scope. Here, we engi…
View article: <i>Plasmodium falciparum</i> Calcium Dependent Protein Kinase 4 is critical for male gametogenesis and transmission to the mosquito vector
<i>Plasmodium falciparum</i> Calcium Dependent Protein Kinase 4 is critical for male gametogenesis and transmission to the mosquito vector Open
Gametocytes of the malaria parasite Plasmodium are taken up by the mosquito vector with an infectious blood meal, representing a critical stage for parasite transmission. Calcium dependent protein kinases (CDPKs) play key roles in calcium-…
View article: A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS Open
Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries …
View article: Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project Open
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and …
View article: Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays Open
BACKGROUND: For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy t…
View article: DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics
DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics Open
Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing …
View article: Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum Open
Our findings demonstrate conclusively that low abundance and upregulated transcripts are preferentially translated, potentially by environment-specific translation systems with distinct ribosomal protein composition. We show that a complex…
View article: Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity
Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity Open
The plasma protein fetuin-A mediates the formation of protein-mineral colloids known as calciprotein particles (CPP)-rapid clearance of these CPP by the reticuloendothelial system prevents errant mineral precipitation and therefore patholo…
View article: PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline
PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline Open
Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modification…
View article: Microvasculopathy, Luminal Calcification and Premature Aging in Fetuin-A Deficient Mice
Microvasculopathy, Luminal Calcification and Premature Aging in Fetuin-A Deficient Mice Open
Objective The plasma protein fetuin-A mediates the formation of protein-mineral colloids known as calciprotein particles (CPP) – rapid clearance of these CPP by the reticuloendothelial system prevents errant mineral precipitation and there…
View article: Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins
Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins Open
Mastitis is a major challenge to bovine health. The detection of sensitive markers for mastitis in dairy herds is of great demand. Suitable biomarkers should be measurable in milk and should report pathogen-specific changes at an early sta…