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Articles tagged: crosslinking

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Posted by Richard Jacob (December 5, 2023)

ABRF iPRG 2023 crosslinking study

One of the great things about the Association of Biomolecular Resource Facilities (ABRF) is their technical studies involving real samples and data. The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year the iPRG group has put together a crosslinking study. The goal is to teach [...]

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Posted by Patrick Emery (December 16, 2022)

Peak picking intact crosslink spectra with Mascot Distiller

There are several important factors to take into account when carrying out peakpicking for an intact crosslinked dataset. You’ll typically be dealing with higher charge state precursors to handle the larger masses of the linked peptides, and the MS/MS spectra are inherently complex, chimeric spectra with fragments from the alpha and beta peptides. To look at the effects of adjusting [...]

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Posted by Ville Koskinen (May 20, 2022)

mzIdentML 1.2

Mascot Server supports several formats for exporting database search results. One of them is the Proteomics Standards Initiative’s mzIdentML. The Mascot 2.8.1 patch release upgrades the file format version to mzIdentML 1.2. You can now export crosslinked search results in XML, CSV, xiVIEW CSV and mzIdentML format. When you export standard database searches, error tolerant searches and spectral library searches, [...]

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Posted by Richard Jacob (March 23, 2022)

Analyzing the disulfide bond structure of the SARS-Cov-2 Spike protein

The SARS-Cov-2 virus has been under intense investigation since its discovery two years ago. Almost every feasible analytical method has been used and according to PubMed, that includes over 3000 proteomics papers. The most important protein immunologically speaking is the spike protein that is involved in the initial binding to the target cells. An example of the more encompassing spike [...]

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Posted by Ville Koskinen (August 19, 2020)

Validating intact crosslinked peptide matches

Intact crosslinked search results are more complex than conventional (non-crosslinked) searches, because there are many more degrees of freedom. The precursor mass could be within tolerance of a looplinked sequence, a linear sequence with monolink and several different alpha-beta candidates. Each possibility is multiplied if you also consider variable modifications like oxidation of methionine. Mascot 2.7 uses the same scoring [...]

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Posted by John Cottrell (February 19, 2020)

Disulfide bond characterisation

Support for matching crosslinked peptides is a new feature in Mascot Server 2.7. The following linkage types can be detected: intralinks – the linked peptides are from the same protein interlinks – the linked peptides are from two different proteins looplinks – connecting two amino acids within a single peptide monolinks – a linker with one end attached and the [...]

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