Lukas Käll
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View article: Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra Open
A fundamental challenge in mass spectrometry-based proteomics is determining which peptide generated a given MS2 spectrum. Peptide sequencing typically relies on matching spectra against a known sequence database, which in some application…
View article: Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry
Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry Open
View article: Open-Source and FAIR Research Software for Proteomics
Open-Source and FAIR Research Software for Proteomics Open
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of…
View article: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry Open
Antibodies are a major component of adaptive immunity against invading pathogens. Here, we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in con…
View article: Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI
Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI Open
Here, we introduce Met-ID, a graphical user interface software designed to efficiently identify metabolites from MALDI-MSI data sets. Met-ID enables annotation of m/z features from any type of MALDI-MSI experiment, involving …
View article: Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra Open
A fundamental challenge in mass spectrometry-based proteomics is determining which peptide generated a given MS2 spectrum. Peptide sequencing typically relies on matching spectra against a known sequence database, which in some application…
View article: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective Open
Antibodies are a major component of adaptive immunity against invading pathogens. Here we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in conv…
View article: Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Author response: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective Open
View article: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective Open
Antibodies are a major component of adaptive immunity against invading pathogens. Here we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in conv…
View article: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry Open
Antibodies are a major component of adaptive immunity against invading pathogens. Here, we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in con…
View article: Open-source and FAIR Research Software for Proteomics
Open-source and FAIR Research Software for Proteomics Open
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of…
View article: Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease
Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease Open
BACKGROUNDMitochondrial diseases belong to the group of inborn errors of metabolism (IEM), with a prevalence of 1 in 2,000-5,000 individuals. They are the most common form of IEM, but, despite advances in next-generation sequencing technol…
View article: ECCB2024: The 23rd European Conference on Computational Biology
ECCB2024: The 23rd European Conference on Computational Biology Open
View article: quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data
quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data Open
View article: Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective
Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry – a perspective Open
Antibodies are a major component of adaptive immunity against invading pathogens. Here we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in conv…
View article: Spatial landmark detection and tissue registration with deep learning
Spatial landmark detection and tissue registration with deep learning Open
Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explor…
View article: Automated model building and protein identification in cryo-EM maps
Automated model building and protein identification in cryo-EM maps Open
View article: Pathway analysis through mutual information
Pathway analysis through mutual information Open
Motivation In pathway analysis, we aim to establish a connection between the activity of a particular biological pathway and a difference in phenotype. There are many available methods to perform pathway analysis, many of them rely on an u…
View article: ProHap enables proteomic database generation accounting for population diversity
ProHap enables proteomic database generation accounting for population diversity Open
Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this infor…
View article: How to train a post-processor for tandem mass spectrometry proteomics database search while maintaining control of the false discovery rate
How to train a post-processor for tandem mass spectrometry proteomics database search while maintaining control of the false discovery rate Open
Decoy-based methods are a popular choice for the statistical validation of peptide detections in tandem mass spectrometry proteomics data. Such methods can achieve a substantial boost in statistical power when coupled with post-processors …
View article: Spatial multimodal analysis of transcriptomes and metabolomes in tissues
Spatial multimodal analysis of transcriptomes and metabolomes in tissues Open
View article: Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides
Retention Time and Fragmentation Predictors Increase Confidence in Identification of Common Variant Peptides Open
Precision medicine focuses on adapting care to the individual profile of patients, for example, accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promise towar…
View article: Spatial landmark detection and tissue registration with deep learning
Spatial landmark detection and tissue registration with deep learning Open
Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explor…
View article: The Association of Biomolecular Resource FacilitiesProteome Informatics Research Group Study on Metaproteomics(iPRG-2020)
The Association of Biomolecular Resource FacilitiesProteome Informatics Research Group Study on Metaproteomics(iPRG-2020) Open
Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sam…
View article: Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides Open
Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides" The database directory contains the FASTA files of the four protein sequence databases u…
View article: Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides
Supplementarty Data: Retention time and fragmentation predictors increase confidence in identification of common variant peptides Open
Supplementary data related to the paper "Retention time and fragmentation predictors increase confidence in identification of common variant peptides" The database directory contains the FASTA files of the four protein sequence databases u…
View article: Automated model building and protein identification in cryo-EM maps
Automated model building and protein identification in cryo-EM maps Open
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in …
View article: Retention time and fragmentation predictors increase confidence in variant peptide identification
Retention time and fragmentation predictors increase confidence in variant peptide identification Open
Precision medicine focuses on adapting care to the individual profile of patients, e.g. accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promises towards this…
View article: Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry
Triqler for Protein Summarization of Data from Data-Independent Acquisition Mass Spectrometry Open
A frequent goal, or subgoal, when processing data from a quantitative shotgun proteomics experiment is a list of proteins that are differentially abundant under the examined experimental conditions. Unfortunately, obtaining such a list is …
View article: Toward an Integrated Machine Learning Model of a Proteomics Experiment
Toward an Integrated Machine Learning Model of a Proteomics Experiment Open
In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals…