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Article ; Online: m-nitrobenzyl alcohol supercharging reagent enhances the chromatographic separation and the charging of disulfide bond linked and His-tag peptides.

Lin, Chia-Wei / Canonica, Fabia / Wüthrich, Simone / Fettelschoss-Gabriel, Antonia / Schlapbach, Ralph / Nanni, Paolo

2024 Volume 1722, Page(s) 464828

Abstract: The linkages of disulfide bond (DSB) play important roles in protein stability and activity. Mass spectrometry-based (MS-based) techniques become accepted tools for DSB analysis in the recent decade. In the bottom-up approach, after enzyme digestion, the ...

Abstract	The linkages of disulfide bond (DSB) play important roles in protein stability and activity. Mass spectrometry-based (MS-based) techniques become accepted tools for DSB analysis in the recent decade. In the bottom-up approach, after enzyme digestion, the neighbouring amino acids of cysteines have great impacts on the physicochemical properties of resulting disulfide bond peptides, determining their retention behaviour on liquid chromatography (LC) and their MS ionization efficiency. In this study, the addition of supercharging reagent in LC mobile phase was used to examine the impact of supercharging reagent on the charge states of disulfide-bond peptides. The results showed that 0.1 % m-nitrobenzyl alcohol (m-NBA) in LC mobile phase increased the sensitivity and charge states of DSB peptides from our model protein, equine Interleukin-5 (eIL5), as well as the resolution of reversed-phase chromatography. Notably, also the sensitivity of C-terminal peptide with His-tag significantly improved. Our findings highlight the effectiveness of employing m-NBA as a supercharging reagent when investigating disulfide-linked peptides and the C-terminal peptide with a His-tag through nano-liquid chromatography mass spectrometry.
MeSH term(s)	Disulfides/chemistry ; Benzyl Alcohols/chemistry ; Benzyl Alcohols/isolation & purification ; Peptides/chemistry ; Peptides/isolation & purification ; Animals ; Horses ; Histidine/chemistry ; Chromatography, Liquid/methods ; Chromatography, Reverse-Phase/methods ; Chromatography, High Pressure Liquid/methods
Chemical Substances	Disulfides ; 3-nitrobenzyl alcohol (F829X990IV) ; Benzyl Alcohols ; Peptides ; Histidine (4QD397987E)
Language	English
Publishing date	2024-03-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2024.464828
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Article: Mass Spectrometry in Proteomics: Technologies, Methods, and Research Applications for the Life Sciences.

Nanni, Paolo / Gehrig, Peter / Schlapbach, Ralph

Chimia

2022 Volume 76, Issue 1-2, Page(s) 73–80

Abstract: Mass spectrometry is a powerful tool in the hand of life science researchers, who constantly develop and apply new methods for the investigation of biomolecules, such as proteins, peptides, metabolites, lipids, and glycans. In this review, we will ... ...

Abstract	Mass spectrometry is a powerful tool in the hand of life science researchers, who constantly develop and apply new methods for the investigation of biomolecules, such as proteins, peptides, metabolites, lipids, and glycans. In this review, we will discuss the importance of mass spectrometry for the life science sector, with a special focus on the most relevant current applications in the field of proteomics. Moreover, we will comment on the factors that research groups should consider when setting up a mass spectrometry laboratory, and on the fundamental role played by academic core facilities and industrial service providers.
Language	English
Publishing date	2022-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1516-7
ISSN	0009-4293
ISSN	0009-4293
DOI	10.2533/chimia.2022.73
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Article ; Online: Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair.

Sobek, Jens / Schlapbach, Ralph

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 22

Abstract: To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence ... ...

Abstract	To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7-8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
MeSH term(s)	Base Pairing ; Base Sequence ; Kinetics ; Oligonucleotides/chemistry ; Oxidation-Reduction ; Single Molecule Imaging ; Spectrometry, Fluorescence ; Surface Plasmon Resonance
Chemical Substances	Oligonucleotides
Language	English
Publishing date	2020-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25225369
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Article ; Online: Tlr4

Ryan, Fari / Francos-Quijorna, Isaac / Hernández-Mir, Gerard / Aquino, Catharine / Schlapbach, Ralph / Bradbury, Elizabeth J / David, Samuel

The Journal of neuroscience : the official journal of the Society for Neuroscience

2024 Volume 44, Issue 6

Abstract: Toll-like receptors (TLRs) play an important role in the innate immune response after CNS injury. Although TLR4 is one of the best characterized, its role in chronic stages after spinal cord injury (SCI) is not well understood. We examined the role of ... ...

Abstract	Toll-like receptors (TLRs) play an important role in the innate immune response after CNS injury. Although TLR4 is one of the best characterized, its role in chronic stages after spinal cord injury (SCI) is not well understood. We examined the role of TLR4 signaling in injury-induced responses at 1 d, 7 d, and 8 weeks after spinal cord contusion injury in adult female TLR4 null and wild-type mice. Analyses include secondary damage, a range of transcriptome and protein analyses of inflammatory, cell death, and extracellular matrix (ECM) molecules, as well as immune cell infiltration and changes in axonal sprouting and locomotor recovery. Lack of TLR4 signaling results in reduced neuronal and myelin loss, reduced activation of NFκB, and decreased expression of inflammatory cytokines and necroptotic cell death pathway at a late time point (8 weeks) after injury. TLR4 null mice also showed reduction of scar-related ECM molecules at 8 weeks after SCI, accompanied by increase in ECM molecules associated with perineuronal nets, increased sprouting of serotonergic fibers, and improved locomotor recovery. These findings reveal novel effects of TLR4 signaling in chronic SCI. We show that TLR4 influences inflammation, cell death, and ECM deposition at late-stage post-injury when secondary injury processes are normally considered to be over. This highlights the potential for late-stage targeting of TLR4 as a potential therapy for chronic SCI.
MeSH term(s)	Mice ; Female ; Animals ; Cytokines/metabolism ; Toll-Like Receptor 4/genetics ; Toll-Like Receptor 4/metabolism ; Spinal Cord Injuries ; Neurons/metabolism ; Inflammation/metabolism ; Mice, Knockout ; Spinal Cord/metabolism ; Recovery of Function/physiology
Chemical Substances	Cytokines ; Toll-Like Receptor 4 ; Tlr4 protein, mouse
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	604637-x
ISSN	1529-2401 ; 0270-6474
ISSN (online)	1529-2401
ISSN	0270-6474
DOI	10.1523/JNEUROSCI.0778-23.2023
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Article ; Online: prolfqua

Wolski, Witold E / Nanni, Paolo / Grossmann, Jonas / d'Errico, Maria / Schlapbach, Ralph / Panse, Christian

Journal of proteome research

2023 Volume 22, Issue 4, Page(s) 1092–1104

Abstract: Mass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. There is a large variety of quantification software and analysis tools. Nevertheless, there is a need ...

Abstract	Mass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. There is a large variety of quantification software and analysis tools. Nevertheless, there is a need for a modular, easy-to-use application programming interface in
MeSH term(s)	Proteomics/methods ; Software ; Proteins/analysis ; Models, Statistical ; Mass Spectrometry/methods
Chemical Substances	Proteins
Language	English
Publishing date	2023-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00441
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Article: Association of proteomic markers with nutritional risk and response to nutritional support: A secondary pilot study of the EFFORT trial using an untargeted proteomics approach

Struja, Tristan / Laczko, Endre / Wolski, Witold / Schlapbach, Ralph / Mueller, Beat / Roschitzki, Bernd / Schuetz, Philipp

Clinical nutrition ESPEN. 2022 Apr., v. 48

2022

Abstract: By means of a structured nutritional support intervention, EFFORT showed a risk reduction for adverse events in medical in-patients. We were interested in the prognostic and therapeutic potential of an untargeted proteomics approach to understand ... ...

Abstract	By means of a structured nutritional support intervention, EFFORT showed a risk reduction for adverse events in medical in-patients. We were interested in the prognostic and therapeutic potential of an untargeted proteomics approach to understand response to nutritional support, risk of 30-day mortality, and distinct patterns in severity of malnutrition risk as assessed by the Nutritional Risk screening (NRS 2002), respectively. From 2,088 patients, we randomly took 120 blood samples drawn before treatment initiation on day 1 after hospital admission. Cases were selected by treatment allocation (nutritional support vs. usual nutrition), NRS 2002, and mortality at 30 days, but not on disease type. We measured proteins by untargeted liquid chromatography mass spectrometry (LC-MS/MS). We found 242 distinct proteins in 120 patients of which 81 (67.5%) survived until day 30. Between group analysis revealed a slight difference between the treatment groups in patients with a NRS 3, but not in those with a higher NRS. C-statistic between non-survivors and survivors at day 30 ranged from 0.60 (95% confidence interval 0.34–0.78) for a combination of 3 proteins/predictors to 0.65 (95% CI 0.53–0.78) for a combination of 32 proteins/predictors. In nutritional support non-survivors, pathway analysis found significant enrichment in pathways for signal transduction, platelet function, immune system regulation, extracellular matrix organization, and integrin cell surface interactions compared to survivors. Within this pilot study using an untargeted proteomics approach, there was only little prognostic and therapeutic potential of proteomics for phenotyping the risk of malnutrition and response to nutritional therapy. The small sample size and high heterogeneity of our population regarding comorbidity burden calls for more targeted approaches in more homogenous populations to understand the true potential of proteomics for individualizing nutritional care. This is a pre-planned secondary analysis of the EFFORT trial (ClinicalTrials.gov NCT02517476).
Keywords	blood ; clinical nutrition ; comorbidity ; confidence interval ; extracellular matrix ; hospitals ; immune system ; integrins ; liquid chromatography ; malnutrition ; mortality ; nutrition risk assessment ; nutritional support ; phenotype ; proteomics ; risk ; risk reduction ; sample size ; signal transduction
Language	English
Dates of publication	2022-04
Size	p. 282-290.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	2405-4577
DOI	10.1016/j.clnesp.2022.01.035
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Association of proteomic markers with nutritional risk and response to nutritional support: A secondary pilot study of the EFFORT trial using an untargeted proteomics approach.

Struja, Tristan / Laczko, Endre / Wolski, Witold / Schlapbach, Ralph / Mueller, Beat / Roschitzki, Bernd / Schuetz, Philipp

Clinical nutrition ESPEN

2022 Volume 48, Page(s) 282–290

Abstract: Background: By means of a structured nutritional support intervention, EFFORT showed a risk reduction for adverse events in medical in-patients. We were interested in the prognostic and therapeutic potential of an untargeted proteomics approach to ... ...

Abstract	Background: By means of a structured nutritional support intervention, EFFORT showed a risk reduction for adverse events in medical in-patients. We were interested in the prognostic and therapeutic potential of an untargeted proteomics approach to understand response to nutritional support, risk of 30-day mortality, and distinct patterns in severity of malnutrition risk as assessed by the Nutritional Risk screening (NRS 2002), respectively. Methods: From 2,088 patients, we randomly took 120 blood samples drawn before treatment initiation on day 1 after hospital admission. Cases were selected by treatment allocation (nutritional support vs. usual nutrition), NRS 2002, and mortality at 30 days, but not on disease type. We measured proteins by untargeted liquid chromatography mass spectrometry (LC-MS/MS). Results: We found 242 distinct proteins in 120 patients of which 81 (67.5%) survived until day 30. Between group analysis revealed a slight difference between the treatment groups in patients with a NRS 3, but not in those with a higher NRS. C-statistic between non-survivors and survivors at day 30 ranged from 0.60 (95% confidence interval 0.34-0.78) for a combination of 3 proteins/predictors to 0.65 (95% CI 0.53-0.78) for a combination of 32 proteins/predictors. In nutritional support non-survivors, pathway analysis found significant enrichment in pathways for signal transduction, platelet function, immune system regulation, extracellular matrix organization, and integrin cell surface interactions compared to survivors. Conclusion: Within this pilot study using an untargeted proteomics approach, there was only little prognostic and therapeutic potential of proteomics for phenotyping the risk of malnutrition and response to nutritional therapy. The small sample size and high heterogeneity of our population regarding comorbidity burden calls for more targeted approaches in more homogenous populations to understand the true potential of proteomics for individualizing nutritional care. Trial registration: This is a pre-planned secondary analysis of the EFFORT trial (ClinicalTrials.gov NCT02517476).
MeSH term(s)	Chromatography, Liquid ; Humans ; Nutritional Support/methods ; Pilot Projects ; Proteomics ; Tandem Mass Spectrometry
Language	English
Publishing date	2022-02-02
Publishing country	England
Document type	Clinical Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2405-4577
ISSN (online)	2405-4577
DOI	10.1016/j.clnesp.2022.01.035
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Article ; Online: Long fragments achieve lower base quality in Illumina paired-end sequencing.

Tan, Ge / Opitz, Lennart / Schlapbach, Ralph / Rehrauer, Hubert

Scientific reports

2019 Volume 9, Issue 1, Page(s) 2856

Abstract: Illumina's technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error rate below 1/1000. However, some ... ...

Abstract	Illumina's technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error rate below 1/1000. However, some paired-end sequencing data show the presence of a subpopulation of reads where the second read (R2) has lower average qualities. We show that the fragment length is a major driver of increased error rates in the R2 reads. Fragments above 500 nt tend to yield lower base qualities and higher error rates than shorter fragments. We use publicly available Illumina data to demonstrate that the fragment length dependency of the R2 read qualities exists in various library protocols, in different labs and using different sequencer models. Our finding extends the understanding of the Illumina read quality and has implications on error models for Illumina reads. It also sheds a light on the importance of controlling the fragment size during library preparation.
MeSH term(s)	Base Sequence ; Gene Library ; High-Throughput Nucleotide Sequencing/instrumentation ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2019-02-27
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/s41598-019-39076-7
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Article: Mass Spectrometric Proteome Analysis of Small Three-Dimensional Microtissues Allows for the Quantitative Description of Toxic Effects of Drugs.

Selevsek, Nathalie / Schlapbach, Ralph

Chimia

2015 Volume 69, Issue 7, Page(s) 494

Language	English
Publishing date	2015-08-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1516-7
ISSN	0009-4293
ISSN	0009-4293
DOI	10.2533/chimia.2015.494
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Article ; Online: Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence.

Sobek, Jens / Schmidt, Marco / Grossmann, Jonas / Rehrauer, Hubert / Schmidt, Lucas / Schlapbach, Ralph

Methods and applications in fluorescence

2020 Volume 8, Issue 3, Page(s) 35010

Abstract: Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial ... ...

Abstract	Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
MeSH term(s)	Carbocyanines/therapeutic use ; Fluorescence ; Humans ; Oligonucleotides/chemistry ; Oxidation-Reduction
Chemical Substances	Carbocyanines ; Oligonucleotides ; cyanine dye 3
Language	English
Publishing date	2020-07-07
Publishing country	England
Document type	Journal Article
ISSN	2050-6120
ISSN (online)	2050-6120
DOI	10.1088/2050-6120/ab947d
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