TY  - JOUR
A1  - Abbas, Ioana M.
A1  - Vranic, Marija
A1  - Hoffmann, Holger
A1  - El-Khatib, Ahmed H.
A1  - Montes-Bayón, María
A1  - Möller, Heiko Michael
A1  - Weller, Michael G.
T1  - Investigations of the Copper Peptide Hepcidin-25 by
LC-MS/MS and NMR⁺
JF  - International Journal of Molecular Sciences
N2  - 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.
KW  - hepcidin-25
KW  - copper
KW  - nickel
KW  - copper complex
KW  - ATCUN motif
KW  - metal complex
KW  - MS
KW  - NMR structure
KW  - metal peptide
KW  - metalloprotein
KW  - metallopeptide
KW  - isomerization
KW  - racemization
KW  - purity
KW  - reference material
Y1  - 2018
U6  - https://doi.org/10.3390/ijms19082271
SN  - 1422-0067
SN  - 1661-6596
VL  - 19
IS  - 8
PB  - Molecular Diversity Preservation International
CY  - Basel
ER  - 
TY  - JOUR
A1  - Hiort, Pauline
A1  - Schlaffner, Christoph N.
A1  - Steen, Judith A.
A1  - Renard, Bernhard Y.
A1  - Steen, Hanno
T1  - multiFLEX-LF: a computational approach to quantify the modification stoichiometries in label-free proteomics data sets
JF  - Journal of proteome research
N2  - 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.
KW  - bioinformatics tool
KW  - label-free quantification
KW  - LC-MS
KW  - MS
KW  - post-translational modification
KW  - modification stoichiometry
KW  - PTM
KW  - quantification
Y1  - 2022
U6  - https://doi.org/10.1021/acs.jproteome.1c00669
SN  - 1535-3893
SN  - 1535-3907
VL  - 21
IS  - 4
SP  - 899
EP  - 909
PB  - American Chemical Society
CY  - Washington
ER  -