The Manchester Peptide Location Fingerprinter Webtool: MPLF

Alexander Eckersley* (Developer), Matiss Ozols (Developer), Michael Sherratt (Developer)

*Corresponding author for this work

Research output: Non-textual formSoftware

Abstract

Webtool URL: https://www.manchesterproteome.manchester.ac.uk/#/MPLF

The MPLF webtool is a publicly available proteomic biomarker discover software capable of the unbiased identification of protein structure-associated changes, such as damage modification in ageing and diseased extracellular matrix proteins. Since launch, MPLF has led to six publications and a successful BBSRC grant application by the developers, been adopted by external collaborators, supported ~1500 users (web-statistics) and achieved peer recognition (highlighted in two journal reviews in Matrix Biology and Molecular Cell Proteomics).

In standard proteomics, proteins are trypsinised, generating peptides whose sequences can be identified and quantified by LC-MS/MS. During this process, most proteins are only partially digested, due to differing solubilities and enzyme susceptibilities related to their 1°-4° structures. By mapping and quantifying peptides within specific regions, MPLF detects statistical differences in regional digestibility along protein structures. By examining how these peptide yield differences coincide with oxidation and protease cleavage sites, and functional regions, and whether the peptides themselves are modified or endogenous cleaved, it is possible to interpret the nature of the damage modifications (e.g. oxidation and fragmentation) and their impact on supramolecular organisation and cell/protein network interactions. A major advantage of MPLF over other analytical approaches is its ability to identify ‘untargeted’ modification-associated changes (i.e., with no prior knowledge of their nature) to individual protein structures in complex tissue proteomes, as well as their potential modifiers and downstream consequences. It is also compatible with standard proteomic MS analysis workflows and datasets and can therefore be used as a proteomic screening tool for identifying modified proteins in addition to changes in composition and protein abundance.
Original languageEnglish
Media of outputOnline
Publication statusPublished - Apr 2021

Keywords

  • Proteomics
  • Extracellular Matrix
  • Software
  • Protein structure
  • Modification

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