Article
Biochemical Research Methods
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M. Franks, Alexander R. Ivanov, Ryan T. Kelly, Luke Khoury, Andrew Leduc, Michael J. MacCoss, Peter Nemes, David H. Perlman, Aleksandra A. Petelski, Christopher M. Rose, Erwin M. Schoof, Jennifer Van Eyk, Christophe Vanderaa, John R. R. Yates III, Nikolai Slavov
Summary: Analyzing proteins from single cells by tandem mass spectrometry (MS) has the potential to accurately quantify thousands of proteins across thousands of single cells. However, various factors affecting experimental design, sample preparation, data acquisition and analysis may undermine the accuracy and reproducibility of the results. Best practices, quality controls, and data-reporting recommendations are proposed to enhance the reliability of quantitative workflows for single-cell proteomics.
Article
Nutrition & Dietetics
Veronica Segura, Angela Ruiz-Carnicer, Irati Mendia, Marta Garzon-Benavides, Angeles E. Pizarro, Isabel Comino, Carolina Sousa
Summary: A gluten-free diet is the only treatment for celiac disease, but adherence can be challenging due to the presence of gluten in many foods. This study proposes the development of an automatable ELISA to monitor adherence to the diet by quantifying urine gluten immunogenic peptides. The assay was validated and found to be stable, and it showed that after 12 months on the diet, only 27% of patients had detectable u-GIP compared to 100% at diagnosis. Therefore, this highly sensitive immunoassay could be used in clinical laboratories to analyze u-GIP from a large number of samples.
Article
Biochemistry & Molecular Biology
Yulia V. Samukhina, Dmitriy D. Matyushin, Oksana I. Grinevich, Aleksey K. Buryak
Summary: The study utilizes deep learning techniques to predict peptide collision cross-section values more accurately compared to previous methods, using a complex structure of convolutional neural networks. By integrating additional information such as chromatographic retention time and ion mobility spectrum, the accuracy of analysis has been significantly improved.
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Nutrition & Dietetics
Sophia Escobar-Correas, James A. Broadbent, Alicja Andraszek, Sally Stockwell, Crispin A. Howitt, Angela Juhasz, Michelle L. Colgrave
Summary: Using shotgun proteomics, gluten-like peptides were identified in ryegrass across different cultivars, showing consistent abundance but were not detected in wheat cultivars. These peptides can be valuable in distinguishing between wheat and ryegrass gluten contamination.
FRONTIERS IN NUTRITION
(2021)
Review
Nutrition & Dietetics
Ana G. Abril, Manuel Pazos, Tomas G. Villa, Pilar Calo-Mata, Jorge Barros-Velazquez, Monica Carrera
Summary: Bioactive peptides have various health benefits and can be identified and quantified through proteomics. They have the potential to be a source of novel drugs and ingredients in food and pharmaceuticals.
Article
Biochemistry & Molecular Biology
Ana G. Abril, Monica Carrera, Karola Bohme, Jorge Barros-Velazquez, Pilar Calo-Mata, Angeles Sanchez-Perez, Tomas G. Villa
Summary: The study utilized LC-ESI-MS/MS for a comprehensive shotgun proteomics characterization of pathogenic Listeria species, identifying numerous important proteins involved in Listeria pathogenicity. This proteomic repository can serve as a foundation for further research on pathogenic Listeria species and the development of novel therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Yuliya Korolkova, Alexander Mikov, Anna Lobas, Elizaveta Solovyeva, Alexey Surin, Yaroslav Andreev, Mikhail Gorshkov, Sergey Kozlov
Summary: This study conducted transcriptome and proteome analysis on the venom of Tibellus oblongus spider, revealing the presence of several new toxins.
Article
Chemistry, Multidisciplinary
Jorunn Stamnaes, Daniel Stray, Maria Stensland, Vikas K. Sarna, Tuula A. Nyman, Knut E. A. Lundin, Ludvig M. Sollid
Summary: In patients with celiac disease (CeD) who have been effectively treated with a gluten-free diet, different degrees of tissue inflammation response are observed after gluten challenge, indicating the presence of low-grade tissue inflammation and antigluten immunity. Histological assessment alone may not be sufficient to evaluate the full recovery and gut mucosal healing of CeD patients. There is a concern that a seemingly proper gluten-free diet may not be able to completely control gut inflammation in all CeD patients.
Article
Biochemistry & Molecular Biology
Gabor Kecskemeti, Edit Toth-Molnar, Tamas Janaky, Zoltan Szabo
Summary: Tear samples are valuable sources of information for precision medicine, and this study evaluates a novel sample collection technique for human tear samples. The results show that this new technique is equally or even more suitable for proteomic sample collection compared to traditional methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Tessa B. Moyer, Wyatt J. Schug, Leslie M. Hicks
Summary: This study utilizes in silico predictions, proteomics, and simulated gastrointestinal digestions to identify digestion resistant cysteine-rich peptides (CRPs) within Amaranthus hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract, providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics, revealing multiple post translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.
Article
Nutrition & Dietetics
Mitchell G. Nye-Wood, Angela Juhasz, Utpal Bose, Michelle L. Colgrave
Summary: This study investigated the proteome profile of a novel wheat flour, revealing a decrease in certain allergenic proteins while an increase in others compared to traditional mixed wheat flour. The novel wheat variety had a 33% reduction in gluten protein content, but showed a 53% increase in allergenic peptides. The importance of proteomic analyses for monitoring immunostimulatory proteins was highlighted in this study.
FRONTIERS IN NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Emmanouil Mavrogeorgis, Harald Mischak, Agnieszka Latosinska, Justyna Siwy, Vera Jankowski, Joachim Jankowski
Summary: In recent years, CE-MS has been increasingly used in clinical research for chronic and age-associated diseases, allowing for comprehensive assessment of small molecular weight proteins and peptides. The study evaluated the analytical performance of CE-MS in terms of reproducibility, variability, and efficiency in peptide detection, showing high correlation among different runs and low variation in signal intensity. These findings support the value of CE-MS for clinical application.
Article
Biochemical Research Methods
Antony McCabe, Andrew R. Jones
Summary: Complex biological samples are often analyzed using mass spectrometry paired with liquid chromatography or gas chromatography in proteomics and metabolomics research. lcmsWorld is a new software that utilizes graphics hardware to quickly examine and compare LC-MS data, providing a more intuitive way to visualize the data.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Food Science & Technology
Huiyan Zhang, Shizhe Qi, Wenhao Yu, Shan Zhao, Yan Jin, Qiancheng Zhao, Yanxia Qi
Summary: In this study, anchovy antimicrobial peptides (AAMPs) were prepared and optimised from anchovy extracts. Proteomics analysis identified 4 unique peptides with inhibitory activity against E. coli and S. aureus. This work established a useful workflow for discovering novel AMPs from fish proteins, which could contribute to the development of effective antibiotics.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Review
Chemistry, Applied
Herbert Wieser, Peter Koehler, Katharina A. Scherf
Summary: This study provides an updated and detailed understanding of the chemistry of wheat gluten proteins, with a focus on their qualitative composition.
Review
Chemistry, Applied
Herbert Wieser, Peter Koehler, Katharina A. Scherf
Summary: The content and composition of wheat gluten proteins are influenced by genetic and environmental factors. This review provides an overview of the latest research on the chemistry of gluten and its relationship with various factors.
Article
Chemistry, Applied
Clemens Schuster, Julien Huen, Katharina Anne Scherf
Summary: This study comprehensively analyzed 82 wheat flours, especially in terms of gluten composition. The results showed that baking quality of flour is the result of a complex combination of different parameters, and there is no significant correlation between protein composition and loaf volume.
Article
Food Science & Technology
Luciana Ribeiro da Silva Lima, Millena Cristina Barros Santos, Carolina Thomaz dos Santos D'Almeida, Luiz Claudio Cameron, Luiz Carlos Gutkoski, Mariana Simoes Larraz Ferreira
Summary: This study characterized the phenolic profile of whole wheat flour from different genotypes and technological qualities. Thirty-eight phenolic compounds were tentatively identified, mainly belonging to the class of bound hydroxycinnamic acids. The use of omics data and multivariate statistical analyses successfully differentiated the phenolic profile of the whole wheat flour samples.
JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
(2023)
Article
Food Science & Technology
Charlotte Dorothea Stemler, Katharina Anne Scherf
Summary: This study analyzed the effects of seven lipases on three different cake formulations and compared them to the emulsifier DATEM. The results showed that both the lipase and the cake formulation had an impact on the batter improvement. The greatest effects were observed in the eggless cake, while lipase reactions seemed to be inhibited in the yeast-based cake. Three lipases in the basic cake and pound cake decreased batter density and stickiness, and caused a liquefaction of the batter.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Chemistry, Physical
Franziska Ersoy, Philine Beinhorn, Kathrin Schalk, Katharina A. Scherf, Ralf G. Berger, Ulrich Krings
Summary: This study demonstrates that a prolyl endopeptidase from Flammulina velutipes (FvpP) can effectively degrade peptides that induce celiac disease. Compared to the commercially available prolyl-specific endopeptidase An-Pep, FvpP has higher effectiveness in peptide degradation. Further clinical studies are needed to evaluate the therapeutic or preventive potential of FvpP for celiac disease.
Article
Food Science & Technology
Tanja Miriam Schirmer, Katharina Anne Scherf
Summary: Food processing conditions and alkali treatment can affect the accurate detection of gluten in baked goods by ELISA. The extraction solvents used in this study showed different performances, but none of them could compensate for the effect of baking on gluten detection. Dough preparation, baking, and alkali treatment decreased protein extractability, especially at high temperatures, due to the formation of gluten crosslinks. The composition of alcohol- and SDS-soluble proteins did not correlate with their extractability. Therefore, gluten extractability rather than composition is crucial for gluten detection in baked goods by ELISA.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Chemistry, Applied
Majlinda Xhaferaj, Gabriella Muskovics, Eszter Schall, Zsuzsanna Bugyi, Sandor Tomoskozi, Katharina A. Scherf
Summary: The study aimed to select representative samples out of 32 rye cultivars for use as reference materials in gluten analysis, in order to ensure the safety of gluten-free products.
Article
Biochemistry & Molecular Biology
Tatiana de Souza Medina, Carolina Thomaz dos Santos D'Almeida, Talita Pimenta do Nascimento, Joel Pimentel de Abreu, Vanessa Rosse de Souza, Diego Calandrini Kalili, Anderson Junger Teodoro, Luiz Claudio Cameron, Maria Gabriela Koblitz, Mariana Simoes Larraz Ferreira
Summary: Untargeted metabolomics is a powerful tool for characterizing a wide range of bioactive natural products from fruit and vegetable by-products. In this study, the metabolomic screening of five fruit and vegetable by-products was conducted to evaluate phenolic compounds. The extraction method was optimized and the total phenolic content and antioxidant activity analyses were used to select the best extractor and ultrasonication time for each by-product. The application of metabolomics increased the understanding of the bioactive potential and valorization of the generated extracts.
Article
Chemistry, Applied
Majlinda Xhaferaj, Gabriella Muskovics, Eszter Schall, Zsuzsanna Bugyi, Sandor Tomoskozi, Katharina A. Scherf
Summary: Celiac disease (CD) can occur when susceptible individuals consume gluten found in wheat, rye, and barley. The lack of specific reference material (RM) for barley results in inaccurate measurement of barley gluten in gluten-free foods. This study aimed to identify representative barley cultivars to establish a new barley RM. The protein composition of the selected cultivars was determined, and eight potential RMs were chosen to improve food safety for CD patients.
Article
Chemistry, Applied
Lynda Abdelbost, Marie-Helene Morel, Talita Pimenta do Nascimento, Luiz-Claudio Cameron, Joelle Bonicel, Mariana Ferreira Simoes Larraz, Hamza Mameri
Summary: Germination is a method to improve the digestibility of kafirin, the sorghum grain storage protein. During germination, the content of free sulfhydryl groups increased, leading to enhanced in vitro protein digestibility. The study also identified the dynamic changes of enzymes and the appearance of aqueous soluble peptides derived from kafirin, which serve as potential biomarkers of kafirin proteolysis. Controlled germination can be a way to improve the nutritional value of sorghum.
Review
Dermatology
Valentina Faihs, Claudia Kugler, Viktoria Schmalhofer, Katharina Anne Scherf, Barbara Lexhaller, Charlotte G. Mortz, Carsten Bindslev-Jensen, Tilo Biedermann, Knut Brockow
Summary: Wheat-dependent exercise-induced anaphylaxis (WDEIA) is an IgE-mediated food allergy that occurs when wheat ingestion is combined with certain cofactors. Diagnosis is established through various tests including serum IgE profile and challenge tests with cofactors. Management involves individual dietary counseling and the provision of emergency treatment options. Further research is needed on sublingual immunotherapy for WDEIA as a potential therapeutic approach. This article provides an overview of the diagnosis and management of WDEIA.
JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT
(2023)
Article
Agriculture, Multidisciplinary
Tanja Miriam Schirmer, Christina Ludwig, Katharina Anne Scherf
Summary: Food processing conditions have a significant impact on the structure, solubility, and accurate detection of gluten proteins. This study investigated the effect of dough, bread, and pretzel making on the composition of different wheat protein fractions. Various analytical methods were used to analyze the fractions obtained from flour, dough, crispbread, bread, and pretzel. The results showed significant changes in the relative abundances of proteins in bread crumb and crust compared to flour, indicating the incorporation of certain gluten proteins into the gluten network through cross-linking.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Food Science & Technology
Nora Jahn, Friedrich H. Longin, Katharina A. Scherf, Sabrina Geisslitz
Summary: This study aims to determine the inhibitory activity of different α-amylases, the content of albumins and globulins (ALGL), and total ATI in wholegrain flour of hexaploid, tetraploid, and diploid wheat species. The results show that the ATI content varied from 0.8% to 20% in different wheat species. There was no correlation between ALGL content and inhibitory activity. The hexaploid cultivars of spelt and common wheat had the highest inhibitory activities against human salivary α-amylase.
CURRENT RESEARCH IN FOOD SCIENCE
(2023)
Article
Chemistry, Applied
Wisse Hermans, Sabrina Geisslitz, Yamina De Bondt, Niels A. Langenaeken, Katharina A. Scherf, Christophe M. Courtin
Summary: This study used laser microdissection and nanoLC-MS/MS to explore the relative differences in protein composition between different parts of wheat endosperm. The results showed that the sub-aleurone contained a higher proportion of gluten proteins than the inner endosperm, with differences in specific protein components.