Explanipedia

Assessment of Reported Error Rates in Crosslinking Mass Spectrometry Open

Lutz Fischer, Lars Kolbowski, Swantje Lenz, James E. Bruce, Robert J. Chalkley , et al. · 2025

We benchmarked eight software tools in crosslinking mass spectrometry (MS) to evaluate their accuracy in detecting protein-protein interactions. Whereas about half performed reliably, others reported up to 31-fold more false interactions t…

mzIdentML 1.3.0 – Essential progress on the support of crosslinking and other identifications based on multiple spectra Open

Colin Combe, Lars Kolbowski, Lutz Fischer, Ville Koskinen, Joshua Klein , et al. · 2024

The mzIdentML data format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0,…

xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data Open

Colin Combe, Martin Graham, Lars Kolbowski, Lutz Fischer, Juri Rappsilber · 2024

Crosslinking mass spectrometry (MS) has emerged as an important technique for elucidating the in-solution structures of protein complexes and the topology of protein-protein interaction networks. However, the expanding user community lacke…

Cleavable Cross-Linkers Redefined by a Novel MS<sup>3</sup>-Trigger Algorithm Open

Lars Kolbowski, Lutz Fischer, Juri Rappsilber · 2023

Cross-linking mass spectrometry (MS) is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable cross-linkers could substantially reduce the associated search space expansion b…

mzIdentML 1.3.0 - Essential progress on the support of crosslinking and other identifications based on multiple spectra Open

Colin Combe, Lars Kolbowski, Lutz Fischer, Ville Koskinen, Joshua Klein , et al. · 2023

The mzIdentML file format, originally developed by the Proteomics Standards Initiative in 2011, is the open XML data standard for peptide and protein identification results coming from mass spectrometry. We present mzIdentML version 1.3.0,…

Light-Induced Orthogonal Fragmentation of Crosslinked Peptides Open

Lars Kolbowski, Adam Belsom, Ana M. Pérez‐López, Tony Ly, Juri Rappsilber · 2023

Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditi…

Cleavable crosslinkers redefined by novel MS3-trigger algorithm Open

Lars Kolbowski, Lutz Fischer, Juri Rappsilber · 2023

Crosslinking MS is currently transitioning from a routine tool in structural biology to enabling structural systems biology. MS-cleavable crosslinkers could substantially reduce the associated search space expansion by allowing an MS3-base…

Improved Peptide Backbone Fragmentation Is the Primary Advantage of MS-Cleavable Crosslinkers Open

Lars Kolbowski, Swantje Lenz, Lutz Fischer, Ludwig Sinn, Francis J. O’Reilly , et al. · 2022

Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of mass spectrometry (MS)-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently, such studies hav…

Improved peptide backbone fragmentation is the primary advantage of MS-cleavable crosslinkers Open

Lars Kolbowski, Swantje Lenz, Lutz Fischer, Ludwig Sinn, Francis J. O’Reilly , et al. · 2021

Proteome-wide crosslinking mass spectrometry studies have coincided with the advent of MS-cleavable crosslinkers that can reveal the individual masses of the two crosslinked peptides. However, recently such studies have also been published…

Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm Open

Lars Kolbowski, Adam Belsom, Juri Rappsilber · 2020

We analyzed the backbone fragmentation behavior of tryptic peptides of a four-protein mixture and of E. coli lysate subjected to ultraviolet photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass s…

Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm Open

Lars Kolbowski, Adam Belsom, Juri Rappsilber · 2020

We analyzed the backbone fragmentation behavior of tryptic peptides of a four protein mixture and of E. coli lysate subjected to Ultraviolet Photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrom…

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data Open

Martin Graham, Colin Combe, Lars Kolbowski, Juri Rappsilber · 2019

xiView provides a common platform for the downstream analysis and visualisation of Crosslinking Mass Spectrometry data. It is independent of the search software used and its input is compliant with the relevant mass spectrometry data stand…

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry Open

Fränze Müller, Lars Kolbowski, Oliver M. Bernhardt, Lukas Reiter, Juri Rappsilber · 2019

xiSPEC: web-based visualization, analysis and sharing of proteomics data Open

Lars Kolbowski, Colin Combe, Juri Rappsilber · 2018

We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported…

Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer Open

Lars Kolbowski, Marta Mendes, Juri Rappsilber · 2017

We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccin…

Lars Kolbowski YOU? Author Swipe