ArticleAnalytical chemistry2017
Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer.
Article in Analytical chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 72 citations in OpenAlex.
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- Interpretation of anomalously long crosslinks in ribosome crosslinking reveals the ribosome interaction in stationary phaseRSC chemical biology · 2022Article
- Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size Exclusion Chromatography for Proteome-wide Cross-Linking Mass Spectrometry.Analytical chemistry · 2022Article
- Mass Spectrometric Identification of a Novel Factor XIIIa Cross-Linking Site in Fibrinogen.Proteomes · 2021Article
- Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses.PLoS pathogens · 2021Article
- New insights into the mechanisms of age-related protein-protein crosslinking in the human lens.Experimental eye research · 2021Review
- Reliable identification of protein-protein interactions by crosslinking mass spectrometry.Nature communications · 2021Article
- Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end.The EMBO journal · 2021Article
- O-Glycosylation Landscapes of SARS-CoV-2 Spike Proteins.Frontiers in chemistry · 2021Article
- Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction.Molecular cell · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
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(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase, and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ∼21% more than the second best, HCD). For the medium complexity sample, the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality. Data are available via ProteomeXchange with identifier PXD006131.
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Registered trials
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