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  • Journal article

  • Erosion of human X chromosome inactivation causes major remodelling of the iPSC proteome

    • Authors : Brenes, Alejandro J; Yoshikawa, Harunori; Bensaddek, Dalila (2020)

  • X chromosome inactivation (XCI) is a dosage compensation mechanism in female mammals whereby genes from one X chromosome are repressed. Analysis of human induced pluripotent stem cell (iPSC) lines using proteomics, RNAseq and polysome profiling showed a major change in the proteome upon XCI erosion. This resulted in amplified RNA and protein expression from X-linked genes. However, increased protein expression was also detected from autosomal genes without&#x...
  • Journal article

  • In silico approach toward the identification of unique peptides from viral protein infection: Application to COVID-19

    • Authors : Orsburn, Benjamin C; Jenkins, Conor; Miller, Sierra M (2020)

  • We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity ...
  • Journal article

  • Integrated metabolomics and proteomics of symptomatic and early pre-symptomatic states of colitis

    • Authors : Shimshoni, Elee; Ghini, Veronica; Solomonov, Inna (2020)

  • Two murine models for colitis were used to study multi-level changes and derive molecular signatures of colitis onset and development. By combining metabolomics data on tissues and fecal extracts with proteomics data on tissues, we provide a comprehensive picture of the metabolic profile of acute and chronic states of the disease, and most importantly, of two early pre-symptomatic states. We show that, increased anaerobic glycolysis, accompanied by alter...
  • Journal article

  • A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

    • Authors : Krasny, Lukas; Bland, Philip; Burns, Jessica (2020)

  • SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method ove...
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  • Solid-Phase Peptide Capture and Release for Bulk and Single-Molecule Proteomics

    • Authors : Howard, Cecil J; Floyd, Brendan M; Bardo, Angela M (2020)

  • The field of proteomics has expanded recently with more sensitive techniques for the bulk measurement of peptides as well as single-molecule techniques. One limiting factor for some of these methods is the need for multiple chemical derivatizations and highly pure proteins free of contaminants. We demonstrate a solid-phase capture strategy suitable for the proteolysis, purification, and subsequent chemical modification of peptides. We use this resin on an...