@article{WildeTreitzKeppleretal.2016,
  author    = {Wilde, Sandra Catharina and Treitz, Christian and Keppler, Julia Katharina and Koudelka, Tomas and Palani, Kalpana and Tholey, Andreas and Rawel, Harshadrai Manilal and Schwarz, Karin},
  title     = {beta-Lactoglobulin as nanotransporter - Part II: Characterization of the covalent protein modification by allicin and diallyl disulfide},
  series = {Food chemistry},
  volume    = {197},
  journal   = {Food chemistry},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0308-8146},
  doi       = {10.1016/j.foodchem.2015.11.011},
  pages     = {1022 -- 1029},
  year      = {2016},
  abstract  = {The whey protein beta-lactoglobulin has been proposed as a transporter for covalent bound bioactive compounds in order to enhance their stability and reduce their sensory perception. The garlic derived compounds allicin and diallyl disulfide were bound covalently to the native and heat denatured protein. The binding site and the influence of the modification on the digestibility were determined by mass spectrometric analysis of the modified beta-lactoglobulin. Further, the conformation of the modified protein was assessed by circular dichroism and dynamic light scattering. The free thiol group of Cys(121) turned out to be the major binding site. After proteolysis with trypsin at pH 7 but not with pepsin at pH 2, a limited transfer to other cysteinyl residues was observed. The covalently bound ligands did not mask any proteolytic cleavage sites of pepsin, trypsin or chymotrypsin. The modified beta-lactoglobulin showed a native like conformation, besides a moderate loosening of protein folding. The covalent binding of organosulfur compounds to beta-lactoglobulin provides a bioactive ingredient without impairing the digestibility and functional properties of the protein. (C) 2015 Elsevier Ltd. All rights reserved.},
  language  = {en}
}
@article{HiortSchlaffnerSteenetal.2022,
  author    = {Hiort, Pauline and Schlaffner, Christoph N. and Steen, Judith A. and Renard, Bernhard Y. and Steen, Hanno},
  title     = {multiFLEX-LF: a computational approach to quantify the modification stoichiometries in label-free proteomics data sets},
  series = {Journal of proteome research},
  volume    = {21},
  journal   = {Journal of proteome research},
  number    = {4},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1535-3893},
  doi       = {10.1021/acs.jproteome.1c00669},
  pages     = {899 -- 909},
  year      = {2022},
  abstract  = {In liquid-chromatography-tandem-mass-spectrometry-based proteomics, information about the presence and stoichiometry ofprotein modifications is not readily available. To overcome this problem,we developed multiFLEX-LF, a computational tool that builds uponFLEXIQuant, which detects modified peptide precursors and quantifiestheir modification extent by monitoring the differences between observedand expected intensities of the unmodified precursors. multiFLEX-LFrelies on robust linear regression to calculate the modification extent of agiven precursor relative to a within-study reference. multiFLEX-LF cananalyze entire label-free discovery proteomics data sets in a precursor-centric manner without preselecting a protein of interest. To analyzemodification dynamics and coregulated modifications, we hierarchicallyclustered the precursors of all proteins based on their computed relativemodification scores. We applied multiFLEX-LF to a data-independent-acquisition-based data set acquired using the anaphase-promoting complex/cyclosome (APC/C) isolated at various time pointsduring mitosis. The clustering of the precursors allows for identifying varying modification dynamics and ordering the modificationevents. Overall, multiFLEX-LF enables the fast identification of potentially differentially modified peptide precursors and thequantification of their differential modification extent in large data sets using a personal computer. Additionally, multiFLEX-LF candrive the large-scale investigation of the modification dynamics of peptide precursors in time-series and case-control studies.multiFLEX-LF is available athttps://gitlab.com/SteenOmicsLab/multiflex-lf.},
  language  = {en}
}