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  - 
TY  - JOUR
A1  - Wilde, Sandra Catharina
A1  - Treitz, Christian
A1  - Keppler, Julia Katharina
A1  - Koudelka, Tomas
A1  - Palani, Kalpana
A1  - Tholey, Andreas
A1  - Rawel, Harshadrai Manilal
A1  - Schwarz, Karin
T1  - beta-Lactoglobulin as nanotransporter - Part II: Characterization of the covalent protein modification by allicin and diallyl disulfide
JF  - Food chemistry
N2  - 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.
KW  - Beta-lactoglobulin
KW  - Covalent modification
KW  - LC-MS
KW  - CD, DLS
KW  - Thiol
KW  - Allicin
KW  - Garlic
KW  - Diallyl disulfide
Y1  - 2016
U6  - https://doi.org/10.1016/j.foodchem.2015.11.011
SN  - 0308-8146
SN  - 1873-7072
VL  - 197
SP  - 1022
EP  - 1029
PB  - Elsevier
CY  - Oxford
ER  -