Project description:Cashew is one of the most prevalent causes of tree nut allergies. However, the cashew proteome is far from complete, which limits the quality of peptide identification in mass spectrometric analyses. In this study, bioinformatics tools were utilized to construct a customized cashew protein database and improve sequence quality for proteins of interest, based on a publicly available cashew genome database. As a result, two additional isoforms for cashew 2S albumins and five other isoforms for cashew 11S proteins were identified, along with several other potential allergens. Using the optimized protein database, the protein profiles of cashew nuts subjected to different oil-roasting conditions (138 °C and 166 °C for 2-10 minutes) were analyzed using discovery LC-MS/MS analysis. The results showed that cashew 2S protein is most heat-stable, followed by 11S and 7S proteins, though protein isoforms might be affected differently. Preliminary target peptide selection indicated that out of the 29 potential targets, 18 peptides were derived from the newly developed database. In the evaluation of thermal processing effects on cashew proteins, several Maillard reaction adducts were also identified. The cashew protein database developed in this study allows for comprehensive analyses of cashew proteome and development of high-quality allergen detection method.

2022-06-07 | PXD027543 | Pride

MS-GF+ makes progress towards a universal database search tool for proteomics.

Project description: Not available

| S-EPMC5036525 | biostudies-literature

ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody on GM06990 Cells [unpublished]

Project description:RNA Polymerase II ChIP-chip using polyclonal antibody (N-20) performed on GM06990 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip

2006-11-30 | GSE6392 | GEO

ENCODE ChIP-chip for RNA Polymerase II using polyclonal antibody (N-20) on HeLaS3 Cells [unpublished]

Project description:RNA Polymerase II ChIP-chip using polyclonal antibody (N-20) performed on HeLaS3 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Pol II-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip

2006-11-30 | GSE6390 | GEO

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

Project description: Not available

| S-EPMC3744223 | biostudies-literature

A commercial antibody to the human condensin II subunit NCAPH2 cross-reacts with a SWI-SNF complex component

Project description:Commercially available antibodies raised against condensin subunits have been widely used to characterise their cellular interactome. Here we have assessed the specificity of a polyclonal antibody (Bethyl A302-276A) that is commonly used as a probe for NCAPH2, the kleisin subunit of condensin II, in mammalian cells. We find that, in addition to its intended target, this antibody cross-reacts with one or more components of the SWI-SNF family of chromatin remodelling complexes in an NCAPH2-independent manner.

2020-12-14 | PXD022620 | Pride

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