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Article ; Online: Discovery of Glycation Products: Unraveling the Unknown Glycation Space Using a Mass Spectral Library from In Vitro Model Systems.

Yan, Yingfei / Hemmler, Daniel / Schmitt-Kopplin, Philippe

2024 Volume 96, Issue 8, Page(s) 3569–3577

Abstract: The nonenzymatic reaction between amino acids (AAs) and reducing sugars, also known as the Maillard reaction, is the primary source of free glycation products (GPs) in vivo and in vitro. The limited number of MS/MS records for GPs in public libraries ... ...

Abstract	The nonenzymatic reaction between amino acids (AAs) and reducing sugars, also known as the Maillard reaction, is the primary source of free glycation products (GPs) in vivo and in vitro. The limited number of MS/MS records for GPs in public libraries hinders the annotation and investigation of nonenzymatic glycation. To address this issue, we present a mass spectral library containing the experimental MS/MS spectra of diverse GPs from model systems. Based on the conceptional reaction processes and structural characteristics of products, we classified GPs into common GPs (CGPs) and modified AAs (MAAs). A workflow for annotating GPs was established based on the structural and fragmentation patterns of each GP type. The final spectral library contains 157 CGPs, 499 MAAs, and 2426 GP spectra with synthetic model system information, retention time, precursor
MeSH term(s)	Humans ; Maillard Reaction ; Tandem Mass Spectrometry ; Metabolomics ; Amino Acids
Chemical Substances	Amino Acids
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c05540
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Article ; Online: DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry.

Weidner, Leopold / Hemmler, Daniel / Rychlik, Michael / Schmitt-Kopplin, Philippe

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 2

Abstract: Motivation: Plasma ionization is rapidly gaining popularity for mass spectrometry (MS)-based studies of volatiles and aerosols. However, data from plasma ionization are delicate to interpret as competing ionization pathways in the plasma create numerous ...

Abstract	Motivation: Plasma ionization is rapidly gaining popularity for mass spectrometry (MS)-based studies of volatiles and aerosols. However, data from plasma ionization are delicate to interpret as competing ionization pathways in the plasma create numerous ion species. There is no tool for detection of adducts and in-source fragments from plasma ionization data yet, which makes data evaluation ambiguous. Summary: We developed DBDIpy, a Python library for processing and formal analysis of untargeted, time-sensitive plasma ionization MS datasets. Its core functionality lies in the identification of in-source fragments and identification of rivaling ionization pathways of the same analytes in time-sensitive datasets. It further contains elementary functions for processing of untargeted metabolomics data and interfaces to an established ecosystem for analysis of MS data in Python. Availability and implementation: DBDIpy is implemented in Python (Version ≥ 3.7) and can be downloaded from PyPI the Python package repository (https://pypi.org/project/DBDIpy) or from GitHub (https://github.com/leopold-weidner/DBDIpy). Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Software ; Ecosystem ; Mass Spectrometry ; Metabolomics ; Gene Library
Language	English
Publishing date	2023-02-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad088
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Article ; Online: Real-Time Monitoring of Miniaturized Thermal Food Processing by Advanced Mass Spectrometric Techniques.

Weidner, Leopold / Hemmler, Daniel / Rychlik, Michael / Schmitt-Kopplin, Philippe

Analytical chemistry

2023 Volume 95, Issue 2, Page(s) 1694–1702

Abstract: Mass spectrometry is a popular and powerful analytical tool to study the effects of food processing. Industrial sampling, real-life sampling, or challenging academic research on process-related volatile and aerosol research often demand flexible, time- ... ...

Abstract	Mass spectrometry is a popular and powerful analytical tool to study the effects of food processing. Industrial sampling, real-life sampling, or challenging academic research on process-related volatile and aerosol research often demand flexible, time-sensitive data acquisition by state-of-the-art mass analyzers. Here, we show a laboratory-scaled, miniaturized, and highly controllable setup for the online monitoring of aerosols and volatiles from thermal food processing based on dielectric barrier discharge ionization (DBDI) mass spectrometry (MS). We demonstrate the opportunities offered by the setup from a foodomics perspective to study emissions from the thermal processing of wheat bread rolls at 210 °C by Fourier transformation ion cyclotron resonance MS. As DBDI is an emerging technology, we compared its ionization selectivity to established atmospheric pressure ionization tools: we found DBDI preferably ionizes saturated, nitrogenous compounds. We likewise identified a sustainable overlap in the selectivity of detected analytes with APCI and electrospray ionization (ESI). Further, we dynamically recorded chemical fingerprints throughout the thermal process. Unsupervised classification of temporal response patterns was used to describe the dynamic nature of the reaction system. Compared to established tools for real-time MS, our setup permits one to monitor chemical changes during thermal food processing at ultrahigh resolution, establishing an advanced perspective for real-time mass spectrometric analysis of food processing.
MeSH term(s)	Mass Spectrometry/methods ; Spectrometry, Mass, Electrospray Ionization
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04874
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Article: HILIC-MS for Untargeted Profiling of the Free Glycation Product Diversity.

Yan, Yingfei / Hemmler, Daniel / Schmitt-Kopplin, Philippe

Metabolites

2022 Volume 12, Issue 12

Abstract: Glycation products produced by the non-enzymatic reaction between reducing carbohydrates and amino compounds have received increasing attention in both food- and health-related research. Although liquid chromatography mass spectrometry (LC-MS) methods ... ...

Abstract	Glycation products produced by the non-enzymatic reaction between reducing carbohydrates and amino compounds have received increasing attention in both food- and health-related research. Although liquid chromatography mass spectrometry (LC-MS) methods for analyzing glycation products already exist, only a few common advanced glycation end products (AGEs) are usually covered by quantitative methods. Untargeted methods for comprehensively analyzing glycation products are still lacking. The aim of this study was to establish a method for simultaneously characterizing a wide range of free glycation products using the untargeted metabolomics approach. In this study, Maillard model systems consisting of a multitude of heterogeneous free glycation products were chosen for systematic method optimization, rather than using a limited number of standard compounds. Three types of hydrophilic interaction liquid chromatography (HILIC) columns (zwitterionic, bare silica, and amide) were tested due to their good retention for polar compounds. The zwitterionic columns showed better performance than the other two types of columns in terms of the detected feature numbers and detected free glycation products. Two zwitterionic columns were selected for further mobile phase optimization. For both columns, the neutral mobile phase provided better peak separation, whereas the acidic condition provided a higher quality of chromatographic peak shapes. The ZIC-cHILIC column operating under acidic conditions offered the best potential to discover glycation products in terms of providing good peak shapes and maintaining comparable compound coverage. Finally, the optimized HILIC-MS method can detect 70% of free glycation product features despite interference from the complex endogenous metabolites from biological matrices, which showed great application potential for glycation research and can help discover new biologically important glycation products.
Language	English
Publishing date	2022-11-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12121179
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Article ; Online: Real-Time Monitoring of Miniaturized Thermal Food Processing by Advanced Mass Spectrometric Techniques

Weidner, Leopold / Hemmler, Daniel / Rychlik, Mike / Schmitt-Kopplin, Philippe

Analytical Chemistry. 2023 Jan. 05, v. 95, no. 2 p.1694-1702

2023

Abstract	Mass spectrometry is a popular and powerful analytical tool to study the effects of food processing. Industrial sampling, real-life sampling, or challenging academic research on process-related volatile and aerosol research often demand flexible, time-sensitive data acquisition by state-of-the-art mass analyzers. Here, we show a laboratory-scaled, miniaturized, and highly controllable setup for the online monitoring of aerosols and volatiles from thermal food processing based on dielectric barrier discharge ionization (DBDI) mass spectrometry (MS). We demonstrate the opportunities offered by the setup from a foodomics perspective to study emissions from the thermal processing of wheat bread rolls at 210 °C by Fourier transformation ion cyclotron resonance MS. As DBDI is an emerging technology, we compared its ionization selectivity to established atmospheric pressure ionization tools: we found DBDI preferably ionizes saturated, nitrogenous compounds. We likewise identified a sustainable overlap in the selectivity of detected analytes with APCI and electrospray ionization (ESI). Further, we dynamically recorded chemical fingerprints throughout the thermal process. Unsupervised classification of temporal response patterns was used to describe the dynamic nature of the reaction system. Compared to established tools for real-time MS, our setup permits one to monitor chemical changes during thermal food processing at ultrahigh resolution, establishing an advanced perspective for real-time mass spectrometric analysis of food processing.
Keywords	aerosols ; analytical chemistry ; atmospheric pressure ; breads ; chemical species ; data collection ; electrospray ionization mass spectrometry ; foodomics ; ionization ; wheat
Language	English
Dates of publication	2023-0105
Size	p. 1694-1702.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04874
Database	NAL-Catalogue (AGRICOLA)

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Article: Elucidation of the non-volatile fingerprint in oven headspace vapor from bread roll baking by ultra-high resolution mass spectrometry

Weidner, Leopold / Yan, Yingfei / Hemmler, Daniel / Rychlik, Michael / Schmitt-Kopplin, Philippe

Food chemistry. 2022 Apr. 16, v. 374

2022

Abstract: Untargeted research on vapor arising during the thermal processing of food has so far focused on volatile aroma compounds. In this study, we present an oven atmosphere sampling strategy to trap headspace aerosols along with semi- and non-volatile ... ...

Abstract	Untargeted research on vapor arising during the thermal processing of food has so far focused on volatile aroma compounds. In this study, we present an oven atmosphere sampling strategy to trap headspace aerosols along with semi- and non-volatile molecules liberated during the baking of wheat bread rolls. The collected vapor condensate was analyzed for its molecular fingerprinting using direct infusion ultra-high resolution mass spectrometry. We detected up to 4,700 molecular species in a vapor sample from bread rolls baked at 230 °C for 15 min. Beyond the global profiling of the underlying matrix, our method can follow complex reaction cascades during the baking process, such as the formation of advanced glycation end-products like maltosine through the interface of trapped vapor. Further, process parameters such as baking temperature and duration were used to model the dynamic liberation of molecules to the oven atmosphere by a response surface methodology approach.
Keywords	advanced glycation end products ; breads ; condensates ; food chemistry ; headspace analysis ; mass spectrometry ; odors ; ovens ; response surface methodology ; temperature ; vapors ; wheat
Language	English
Dates of publication	2022-0416
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2021.131618
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Open Search of Peptide Glycation Products from Tandem Mass Spectra.

Berger, Michelle T / Hemmler, Daniel / Diederich, Philippe / Rychlik, Michael / Marshall, James W / Schmitt-Kopplin, Philippe

Analytical chemistry

2022 Volume 94, Issue 15, Page(s) 5953–5961

Abstract: Identification of chemically modified peptides in mass spectrometry (MS)-based glycation studies is a crucial yet challenging task. There is a need to establish a mode for matching tandem mass spectrometry (MS/MS) data, allowing for both known and ... ...

Abstract	Identification of chemically modified peptides in mass spectrometry (MS)-based glycation studies is a crucial yet challenging task. There is a need to establish a mode for matching tandem mass spectrometry (MS/MS) data, allowing for both known and unknown peptide glycation modifications. We present an open search approach that uses classic and modified peptide fragment ions. The latter are shifted by the mass delta of the modification. Both provide key structural information that can be used to assess the peptide core structure of the glycation product. We also leverage redundant neutral losses from the modification side chain, introducing a third ion class for matching referred to as characteristic fragment ions. We demonstrate that peptide glycation product MS/MS spectra contain multidimensional information and that most often, more than half of the spectral information is ignored if no attempt is made to use a multi-step matching algorithm. Compared to regular and/or modified peptide ion matching, our triple-ion strategy significantly increased the median interpretable fraction of the glycation product MS/MS spectra. For reference, we apply our approach for Amadori product characterization and identify all established diagnostic ions automatically. We further show how this method effectively applies the open search concept and allows for optimized elucidation of unknown structures by presenting two hitherto undescribed peptide glycation modifications with a delta mass of 102.0311 and 268.1768 Da. We characterize their fragmentation signature by integration with isotopically labeled glycation products, which provides high validity for non-targeted structure identification.
MeSH term(s)	Glycosylation ; Ions ; Peptide Fragments ; Peptides/chemistry ; Tandem Mass Spectrometry/methods
Chemical Substances	Ions ; Peptide Fragments ; Peptides
Language	English
Publishing date	2022-04-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00388
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Article ; Online: Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression

Han, Yongtao / Haouel, Amira / Georgii, Elisabeth / Priego-Cubero, Santiago / Wurm, Christoph J. / Hemmler, Daniel / Schmitt-Kopplin, Philippe / Becker, Claude / Durner, Jörg / Lindermayr, Christian

Genes (Basel). 2023 May 30, v. 14, no. 6

2023

Abstract: Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase subfamily HD2s is ... ...

Abstract	Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase subfamily HD2s is repressed by ABA in Arabidopsis. However, little is known about the molecular relationship between HD2A/HD2B and ABA during the vegetative phase. Here, we describe that the hd2ahd2b mutant shows hypersensitivity to exogenous ABA during the germination and post-germination period. Additionally, transcriptome analyses revealed that the transcription of ABA-responsive genes was reprogrammed and the global H4K5ac level is specifically up-regulated in hd2ahd2b plants. ChIP-Seq and ChIP-qPCR results further verified that both HD2A and HD2B could directly and specifically bind to certain ABA-responsive genes. As a consequence, Arabidopsis hd2ahd2b plants displayed enhanced drought resistance in comparison to WT, which is consistent with increased ROS content, reduced stomatal aperture, and up-regulated drought-resistance-related genes. Moreover, HD2A and HD2B repressed ABA biosynthesis via the deacetylation of H4K5ac at NCED9. Taken together, our results indicate that HD2A and HD2B partly function through ABA signaling and act as negative regulators during the drought resistance response via the regulation of ABA biosynthesis and response genes.
Keywords	Arabidopsis ; biosynthesis ; chromatin immunoprecipitation ; drought tolerance ; genes ; germination ; histone deacetylase ; histones ; hypersensitivity ; mutants ; stomatal movement ; transcription (genetics) ; transcriptome
Language	English
Dates of publication	2023-0530
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14061199
Database	NAL-Catalogue (AGRICOLA)

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Article: Open Search of Peptide Glycation Products from Tandem Mass Spectra

Berger, Michelle T. / Hemmler, Daniel / Diederich, Philippe / Rychlik, Michael / Marshall, James W. / Schmitt-Kopplin, Philippe

Analytical chemistry. 2022 Apr. 07, v. 94, no. 15

2022

Abstract	Identification of chemically modified peptides in mass spectrometry (MS)-based glycation studies is a crucial yet challenging task. There is a need to establish a mode for matching tandem mass spectrometry (MS/MS) data, allowing for both known and unknown peptide glycation modifications. We present an open search approach that uses classic and modified peptide fragment ions. The latter are shifted by the mass delta of the modification. Both provide key structural information that can be used to assess the peptide core structure of the glycation product. We also leverage redundant neutral losses from the modification side chain, introducing a third ion class for matching referred to as characteristic fragment ions. We demonstrate that peptide glycation product MS/MS spectra contain multidimensional information and that most often, more than half of the spectral information is ignored if no attempt is made to use a multi-step matching algorithm. Compared to regular and/or modified peptide ion matching, our triple-ion strategy significantly increased the median interpretable fraction of the glycation product MS/MS spectra. For reference, we apply our approach for Amadori product characterization and identify all established diagnostic ions automatically. We further show how this method effectively applies the open search concept and allows for optimized elucidation of unknown structures by presenting two hitherto undescribed peptide glycation modifications with a delta mass of 102.0311 and 268.1768 Da. We characterize their fragmentation signature by integration with isotopically labeled glycation products, which provides high validity for non-targeted structure identification.
Keywords	algorithms ; analytical chemistry ; glycation ; isotope labeling ; peptides ; tandem mass spectrometry
Language	English
Dates of publication	2022-0407
Size	p. 5953-5961.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00388
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Molecular characterization of sequence-driven peptide glycation.

Berger, Michelle T / Hemmler, Daniel / Walker, Alesia / Rychlik, Michael / Marshall, James W / Schmitt-Kopplin, Philippe

Scientific reports

2021 Volume 11, Issue 1, Page(s) 13294

Abstract: Peptide glycation is an important, yet poorly understood reaction not only found in food but also in biological systems. The enormous heterogeneity of peptides and the complexity of glycation reactions impeded large-scale analysis of peptide derived ... ...

Abstract	Peptide glycation is an important, yet poorly understood reaction not only found in food but also in biological systems. The enormous heterogeneity of peptides and the complexity of glycation reactions impeded large-scale analysis of peptide derived glycation products and to understand both the contributing factors and how this affects the biological activity of peptides. Analyzing time-resolved Amadori product formation, we here explored site-specific glycation for 264 peptides. Intensity profiling together with in-depth computational sequence deconvolution resolved differences in peptide glycation based on microheterogeneity and revealed particularly reactive peptide collectives. These peptides feature potentially important sequence patterns that appear in several established bio- and sensory-active peptides from independent sources, which suggests that our approach serves system-wide applicability. We generated a pattern peptide map and propose that in peptide glycation the herein identified molecular checkpoints can be used as indication of sequence reactivity.
MeSH term(s)	Amino Acid Sequence ; Gas Chromatography-Mass Spectrometry ; Humans ; Mass Spectrometry ; Monosaccharides/metabolism ; Peptides/genetics ; Peptides/metabolism
Chemical Substances	Monosaccharides ; Peptides
Language	English
Publishing date	2021-06-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-92413-7
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