@article{AbbasVranicHoffmannetal.2018,
  author    = {Abbas, Ioana M. and Vranic, Marija and Hoffmann, Holger and El-Khatib, Ahmed H. and Montes-Bay{\´o}n, Mar{\´i}a and M{\"o}ller, Heiko Michael and Weller, Michael G.},
  title     = {Investigations of the Copper Peptide Hepcidin-25 by LC-MS/MS and NMR⁺},
  series = {International Journal of Molecular Sciences},
  volume    = {19},
  journal   = {International Journal of Molecular Sciences},
  number    = {8},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {1422-0067},
  doi       = {10.3390/ijms19082271},
  pages     = {16},
  year      = {2018},
  abstract  = {Hepcidin-25 was identified as themain iron regulator in the human body, and it by binds to the sole iron-exporter ferroportin. Studies showed that the N-terminus of hepcidin is responsible for this interaction, the same N-terminus that encompasses a small copper(II) binding site known as the ATCUN (amino-terminal Cu(II)- and Ni(II)-binding) motif. Interestingly, this copper-binding property is largely ignored in most papers dealing with hepcidin-25. In this context, detailed investigations of the complex formed between hepcidin-25 and copper could reveal insight into its biological role. The present work focuses on metal-bound hepcidin-25 that can be considered the biologically active form. The first part is devoted to the reversed-phase chromatographic separation of copper-bound and copper-free hepcidin-25 achieved by applying basic mobile phases containing 0.1\% ammonia. Further, mass spectrometry (tandemmass spectrometry (MS/MS), high-resolutionmass spectrometry (HRMS)) and nuclear magnetic resonance (NMR) spectroscopy were employed to characterize the copper-peptide. Lastly, a three-dimensional (3D)model of hepcidin-25with bound copper(II) is presented. The identification of metal complexes and potential isoforms and isomers, from which the latter usually are left undetected by mass spectrometry, led to the conclusion that complementary analytical methods are needed to characterize a peptide calibrant or referencematerial comprehensively. Quantitative nuclear magnetic resonance (qNMR), inductively-coupled plasma mass spectrometry (ICP-MS), ion-mobility spectrometry (IMS) and chiral amino acid analysis (AAA) should be considered among others.},
  language  = {en}
}
@misc{AbbasVranicHoffmannetal.2019,
  author    = {Abbas, Ioana M. and Vranic, Marija and Hoffmann, Holger and El-Khatib, Ahmed H. and Montes-Bay{\´o}n, Mar{\´i}a and M{\"o}ller, Heiko Michael and Weller, Michael G.},
  title     = {Investigations of the Copper Peptide Hepcidin-25 by LC-MS/MS and NMR⁺},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {701},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42792},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427926},
  year      = {2019},
  abstract  = {Hepcidin-25 was identified as themain iron regulator in the human body, and it by binds to the sole iron-exporter ferroportin. Studies showed that the N-terminus of hepcidin is responsible for this interaction, the same N-terminus that encompasses a small copper(II) binding site known as the ATCUN (amino-terminal Cu(II)- and Ni(II)-binding) motif. Interestingly, this copper-binding property is largely ignored in most papers dealing with hepcidin-25. In this context, detailed investigations of the complex formed between hepcidin-25 and copper could reveal insight into its biological role. The present work focuses on metal-bound hepcidin-25 that can be considered the biologically active form. The first part is devoted to the reversed-phase chromatographic separation of copper-bound and copper-free hepcidin-25 achieved by applying basic mobile phases containing 0.1\% ammonia. Further, mass spectrometry (tandemmass spectrometry (MS/MS), high-resolutionmass spectrometry (HRMS)) and nuclear magnetic resonance (NMR) spectroscopy were employed to characterize the copper-peptide. Lastly, a three-dimensional (3D)model of hepcidin-25with bound copper(II) is presented. The identification of metal complexes and potential isoforms and isomers, from which the latter usually are left undetected by mass spectrometry, led to the conclusion that complementary analytical methods are needed to characterize a peptide calibrant or referencematerial comprehensively. Quantitative nuclear magnetic resonance (qNMR), inductively-coupled plasma mass spectrometry (ICP-MS), ion-mobility spectrometry (IMS) and chiral amino acid analysis (AAA) should be considered among others.},
  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}
}