Ghent University Academic Bibliography

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- Book Chapter
Targeted profiling of protein phosphorylation in plants

Xiangyu Xu (UGent) , Kris Gevaert (UGent) , Ive De Smet (UGent) and Lam Dai Vu (UGent)

(2023) Mass spectrometry-based proteomics. In Methods in Molecular Biology 2718. p.167-179
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- Book Chapter
Increasing the overall proteome coverage by combining protein digestion by Tryp-N and trypsin

Jade Hawksworth (UGent) , Lode Denolf (UGent) , Evy Timmerman (UGent) and Kris Gevaert (UGent)

(2023) Mass spectrometry-based proteomics. In Methods in Molecular Biology 2718. p.1-10
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- Book Chapter
A decoupled Virotrap approach to study the interactomes of N-terminal proteoforms

Annelies Bogaert (UGent) , Tessa Van de Steene (UGent) , Marnik Vuylsteke (UGent) , Sven Eyckerman (UGent) and Kris Gevaert (UGent)

(2023) Methods in enzymology. In Modifications and targeting of protein termini : part A 684. p.253-287
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- Miscellaneous
Methods in phytohormone detection and quantification: 2022

Da Cao (UGent) and Man He

(2023) FRONTIERS IN PLANT SCIENCE. 14.
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- Journal Article
- A1
- open access
Proteomics standards initiative at twenty years : current activities and future work

Eric W. Deutsch, Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, et al.

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.287-301
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- Journal Article
- A1
Identification of new telomere- and telomerase-associated autoantigens in systemic sclerosis

JB Vulsteke, Vanessa Smith (UGent) , Carolien Bonroy (UGent) , R Derua, D Blockmans, P De Haes, S Vanderschueren, JL Lenaerts, KG Claeys, WA Wuyts, et al.

(2023) JOURNAL OF AUTOIMMUNITY. 135.
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- Book Chapter
Cataloguing protein complexes in planta using TurboID-catalyzed proximity labeling

Lore Gryffroy (UGent) , Joren De Ryck (UGent) , Veronique Jonckheere (UGent) , Sofie Goormachtig (UGent) , Alain Goossens (UGent) and Petra Van Damme (UGent)

(2023) Protein-protein interactions : methods and protocols. In Methods in Molecular Biology 2690. p.311-334
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- Journal Article
- A1
- open access
Toward an integrated machine learning model of a proteomics experiment

Benjamin A. Neely, Viktoria Dorfer, Lennart Martens (UGent) , Isabell Bludau, Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) , Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, et al.

(2023) JOURNAL OF PROTEOME RESEARCH. 22(3). p.681-696
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- Journal Article
- A1
- open access
Evaluation of alternative gas chromatographic and mass spectrometric behaviour of trimethylsilyl-derivatives of non-hydrolysed sulfated anabolic steroids

Aðalheiður Dóra Albertsdóttir (UGent) , Wim Van Gansbeke (UGent) , Peter Van Eenoo (UGent) and Michaël Polet (UGent)

(2023) DRUG TESTING AND ANALYSIS. 15(11-12). p.1344-1355
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- Conference Paper
- C3
Universal at-line microbial fermentation monitoring through advances in rapid ambient ionisation mass spectrometry-based metabolomics

Nicolas de Fooz (UGent) , Marilyn De Graeve (UGent) , Pablo Vangeenderhuysen (UGent) , Karolien Maes, Sophie Roelants (UGent) , Sofie De Maeseneire (UGent) , Wim Soetaert (UGent) and Lynn Vanhaecke (UGent)

(2023) Benelux Metabolomics Days 2023, Abstracts.
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- Journal Article
- A1
- open access
Recent advances in high-throughput biofluid metabotyping by direct infusion and ambient ionization mass spectrometry

Vera Plekhova (UGent) , Kimberly De Windt (UGent) , Margot De Spiegeleer (UGent) , Marilyn De Graeve (UGent) and Lynn Vanhaecke (UGent)

(2023) TRAC-TRENDS IN ANALYTICAL CHEMISTRY. 168.
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- Journal Article
- A1
- open access
Quality control for the target decoy approach for peptide identification

Elke Debrie (UGent) , Milan Malfait (UGent) , Ralf Gabriels (UGent) , Arthur Declercq (UGent) , Adriaan Sticker, Lennart Martens (UGent) and Lieven Clement (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.350-358
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- Journal Article
- A1
- open access
Proteomic comparison between non-purified cerebrospinal fluid and cerebrospinal fluid-derived extracellular vesicles from patients with Alzheimer's, Parkinson's and Lewy body dementia

Yael Hirschberg, Natalia Valle-Tamayo, Oriol Dols-Icardo, Sebastiaan Engelborghs, Bart Buelens, Roosmarijn Vandenbroucke (UGent) , Yannick Vermeiren, Kurt Boonen and Inge Mertens

(2023) JOURNAL OF EXTRACELLULAR VESICLES. 12(12).
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- Book Chapter
Virotrap: Trapping Protein Complexes in Virus-Like Particles

Georgios Moschonas (UGent) , Margaux De Meyer (UGent) , Delphine De Sutter (UGent) , Evy Timmerman (UGent) , Petra Van Damme (UGent) and Sven Eyckerman (UGent)

(2023) Methods in Molecular Biology. In Mass Spectrometry-Based Proteomics p.53-71
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- Journal Article
- A1
A bioanalytical screening method for Enterococcus faecalis RNPP-type quorum sensing peptides in murine feces

Frederick Verbeke (UGent) , Nathan Debunne (UGent) , Yorick Janssens (UGent) , Bart De Spiegeleer (UGent) and Evelien Wynendaele (UGent)

(2022) BIOANALYSIS. 14(3). p.151-167
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- PhD Thesis
- open access
Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ralf Gabriels (UGent)

(2022)
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- Book Chapter
Characterization of RBPome in oxidative stress conditions

Zhicheng Zhang (UGent) , Evy Timmerman (UGent) , Francis Impens (UGent) and Frank Van Breusegem (UGent)

(2022) Reactive oxygen species in plants : methods and protocols. In Methods in Molecular Biology 2526. p.259-275
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- Journal Article
- A1
Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samples

Liesl Janssens (UGent) , Dimitri Boeckaerts (UGent) , Simon Hudson, Daria Morozova, Annelies Cannaert (UGent) , David M. Wood, Caitlin Wolfe, Bernard De Baets (UGent) , Michiel Stock (UGent) , Paul, I Dargan, et al.

(2022) CLINICAL CHEMISTRY. 68(7). p.906-916
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- Journal Article
- A1
- open access
Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay Shiferaw, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Tim Van Den Bossche (UGent) , Elien Vandermarliere (UGent) , Lennart Martens (UGent) and Pieter-Jan Volders (UGent)

(2022) JOURNAL OF PROTEOME RESEARCH. 21(5). p.1365-1370
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- Journal Article
- A1
- open access
It is never too late for a cocktail : development and analytical characterization of fixed-dose antibody combinations

Dennis Krieg, Gerhard Winter and Hristo Svilenov (UGent)

(2022) JOURNAL OF PHARMACEUTICAL SCIENCES. 111(8). p.2149-2157
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- Journal Article
- A1
- open access
Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics

Pieter Vervaeke (UGent) , S.E. Borgos, Niek Sanders (UGent) and F. Combes

(2022) ADVANCED DRUG DELIVERY REVIEWS. 184.
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- Journal Article
- A1
- open access
A review of sample preparation for purification of microRNAs and analysis by mass spectrometry methods

Hiba Salim, Roger Peró Gascón (UGent) , Laura Pont, Estela Giménez and Fernando Benavente

(2022) MICROCHEMICAL JOURNAL. 182.
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- Journal Article
- A1
- open access
Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche (UGent) , Ralf Gabriels (UGent) , Arshika Yalavarthi, Yasset Perez-Riverol, et al.

(2022) JOURNAL OF PROTEOME RESEARCH. 21(4). p.1189-1195
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- Journal Article
- A1
A comprehensive evaluation of consensus spectrum generation methods in proteomics

Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, Julia A. Bubis, Ralf Gabriels (UGent) , Henry Webel, et al.

(2022) JOURNAL OF PROTEOME RESEARCH. 21(6). p.1566-1574
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- Book Chapter
On-line immobilized enzyme microreactor capillary zone electrophoresis-mass spectrometry for peptide mapping

Roger Peró Gascón (UGent) , Laura Pont, Estela Giménez, Victoria Sanz-Nebot and Fernando Benavente

(2022) Capillary electrophoresis-mass spectrometry : methods and protocols. In Methods in Molecular Biology p.77-91
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- Journal Article
- A1
- open access
Proteomic comparison of three wild-type pseudorabies virus strains and the attenuated bartha strain reveals reduced incorporation of several tegument proteins in bartha virions

Jonas Delva (UGent) , Simon Daled (UGent) , Cliff Van Waesberghe (UGent) , Ruben Almey (UGent) , Robert J. J. Jansens, Dieter Deforce (UGent) , Maarten Dhaenens (UGent) and Herman Favoreel (UGent)

(2022) JOURNAL OF VIROLOGY. 96(24).
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- Journal Article
- A1
- open access
New applications of advanced instrumental techniques for the characterization of food allergenic proteins

Sara Benedé, Daniel Lozano-Ojalvo, Susana Cristobal, Joana Costa, Enza D’Auria, Tanja Cirkovic Velickovic (UGent) , María Garrido-Arandia, Sibel Karakaya, Isabel Mafra, Gabriel Mazzucchelli, et al.

(2022) CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION. 62(31). p.8686-8702
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- Conference Paper
- C3
High throughput analytical report writing in R : a case study of validating an LC-MS method for the quantification of amoxicillin in human plasma

Pieter-Jan De Sutter (UGent) , Elke Gasthuys (UGent) , An Vermeulen (UGent) and Jan Van Bocxlaer (UGent)

(2022) 24th International Reid Bioanalytical Forum, Abstracts.
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- Journal Article
- A1
- open access
Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Sandrien Desmet (UGent) , Yvan Saeys (UGent) , Kevin Verstaen (UGent) , Rebecca Dauwe (UGent) , Hoon Kim, Claudiu Niculaes (UGent) , Atsushi Fukushima, Geert Goeminne (UGent) , Ruben Vanholme (UGent) , John Ralph, et al.

(2021) COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. 19. p.1127-1144
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- Journal Article
- A1
Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)

T Garrigos, C Neuwirth, A Chapuis, J Bador, L Amoureux, E Barbier, J Caillon, E Cardot-Martin, V Cattoir, A Doléans-Jordheim, et al.

(2021) CLINICAL MICROBIOLOGY AND INFECTION. 27(1). p.126.e1-126.e5
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- Journal Article
- A1
- open access
Proteome profiling of RNF213 depleted cells reveals nitric oxide regulator DDAH1 antilisterial activity

Lia Martina, Caroline Asselman (UGent) , Fabien Henri Thery (UGent) , Katie Boucher (UGent) , Louis Delhaye (UGent) , Teresa Maia (UGent) , Bart Dermaut (UGent) , Sven Eyckerman (UGent) and Francis Impens (UGent)

(2021) FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY. 11.
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- Miscellaneous
- open access
Add mass spectrometry to the pandemic toolbox

Bart Van Puyvelde (UGent) and Maarten Dhaenens (UGent)

(2021) ELIFE. 10.
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- Journal Article
- A1
- open access
Identification of non-canonical translation products in C. elegans using tandem mass spectrometry

Bhavesh S. Parmar, Marlies Peeters (UGent) , Kurt Boonen, Ellie C. Clark, Geert Baggerman, Gerben Menschaert (UGent) and Liesbet Temmerman

(2021) FRONTIERS IN GENETICS. 12.
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- Journal Article
- A1
Doping control analysis of small peptides : a decade of progress

Péter Judák, Simone Esposito, Gilles Coppieters (UGent) , Peter Van Eenoo (UGent) and Koen Deventer (UGent)

(2021) JOURNAL OF CHROMATOGRAPHY B. 1173.
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- Journal Article
- A1
- open access
Hepatic cytochrome P450 abundance and activity in the developing and adult Gottingen Minipig : Pivotal data for PBPK modeling

Laura Buyssens, Laura De Clerck (UGent) , Wim Schelstraete, Maarten Dhaenens (UGent) , Dieter Deforce (UGent) , Miriam Ayuso, Chris Van Ginneken and Steven Van Cruchten

(2021) FRONTIERS IN PHARMACOLOGY. 12.
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- Journal Article
- A2
- open access
Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions

Simon Daled (UGent) , Sander Willems, Bart Van Puyvelde (UGent) , Laura Corveleyn (UGent) , Sigrid Verhelst (UGent) , Laura De Clerck (UGent) , Dieter Deforce (UGent) and Maarten Dhaenens (UGent)

(2021) PROTEOMES. 9(2).
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- Miscellaneous
Mass spectrometry-based clinical proteomics : a revival

Jarne Pauwels (UGent) and Kris Gevaert (UGent)

(2021) EXPERT REVIEW OF PROTEOMICS. 18(6). p.411-414
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- Journal Article
- A1
- open access
Proteomics mapping of the ISGylation landscape in innate immunity

Fabien Henri Thery (UGent) , Denzel Eggermont (UGent) and Francis Impens (UGent)

(2021) FRONTIERS IN IMMUNOLOGY. 12.
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- Journal Article
- A1
Sample preparation free mass spectrometry using laser-assisted rapid evaporative ionization mass spectrometry : applications to microbiology, metabolic biofluid phenotyping, and food authenticity

Simon J. S. Cameron, Alvaro Perdones-Montero, Lieven Van Meulebroek (UGent) , Adam Burke, Kate Alexander-Hardiman, Daniel Simon, Richard Schaffer, Julia Balog, Tamas Karancsi, Tony Rickards, et al.

(2021) JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY. 32(6). p.1393-1401
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- Journal Article
- A2
- open access
Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van Puyvelde (UGent) , Katleen Van Uytfanghe (UGent) , Olivier Tytgat (UGent) , Laurence Van Oudenhove, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Simon Daled (UGent) , Tim Van Den Bossche (UGent) , Pathmanaban Ramasamy (UGent) , Sigrid Verhelst (UGent) , et al.

(2021) JACS AU. 1(6). p.750-765
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- Journal Article
- A1
Development of methods for Mg, Sr and Pb isotopic analysis of crude oil by MC-ICP-MS : addressing the challenges of sample decomposition

Alessandra S. Henn, Stepan M. Chernonozhkin (UGent) , Frank Vanhaecke (UGent) and Erico M. M. Flores

(2021) JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY. 36(7). p.1478-1488
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- Journal Article
- A2
Rapid screening of diverse biotransformations for enzyme evolution

Emily E. Kempa, James L. Galman, Fabio Parmeggiani, James R. Marshall, Julien Malassis, Clement Q. Fontenelle, Jean-Baptiste Vendeville, Bruno Linclau (UGent) , Simon J. Charnock, Sabine L. Flitsch, et al.

(2021) JACS AU. 1(4). p.508-516
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- Journal Article
- A1
Surface coat proteins of the potato cyst nematode, Globodera rostochiensis

James A. Price, Terry K. Smith and John Jones (UGent)

(2021) NEMATOLOGY. 23(1). p.113-123
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- Journal Article
- A1
- open access
Development and application of an analytical method to quantify odour removal in plastic waste recycling processes

Ruben Demets (UGent) , Martijn Roosen (UGent) , Lore Vandermeersch (UGent) , Kim Ragaert (UGent) , Christophe Walgraeve (UGent) and Steven De Meester (UGent)

(2020) RESOURCES CONSERVATION AND RECYCLING. 161.
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- Journal Article
- A1
Urinary detection of rapid‐acting insulin analogues in healthy humans

Péter Judák, Gilles Coppieters (UGent) , Bruno Lapauw (UGent) , Peter Van Eenoo (UGent) and Koen Deventer (UGent)

(2020) DRUG TESTING AND ANALYSIS. 12(11-12). p.1629-1635
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- Journal Article
- A1
Characterization of the new isotopic reference materials IRMM-524A and ERM-AE143 for Fe and Mg isotopic analysis of geological and biological samples

Claudia González de Vega (UGent) , Stepan M. Chernonozhkin (UGent) , Rosa Grigoryan, Marta Costas Rodriguez (UGent) and Frank Vanhaecke (UGent)

(2020) JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY. 35(11). p.2517-2529
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- Journal Article
- A1
Three decades of listeriology through the prism of technological advances

Francis Impens (UGent) and Olivier Dussurget

(2020) CELLULAR MICROBIOLOGY. 22(4).
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- Journal Article
- A1
Comparative study of concatemer efficiency as an isotope-labelled internal standard for allergen quantification

M Gavage, K Van Vlierberghe, C Van Poucke, M De Loose, Kris Gevaert (UGent) , M Dieu, P Renard, T Arnould, P Filee and N Gillard

(2020) FOOD CHEMISTRY. 332.
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- Journal Article
- A1
Next-generation protein analysis in the pathology department

Melek Ahmed, Glenn Broeckx, Geert Baggerman, Karin Schildermans, Patrick Pauwels, Amaryllis H. Van Craenenbroeck and Amélie Dendooven (UGent)

(2020) JOURNAL OF CLINICAL PATHOLOGY. 73(1). p.1-6
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- Journal Article
- A1
- open access
Comparison of capillary electrophoresis and zwitterionic-hydrophilic interaction capillary liquid chromatography with ultraviolet and mass spectrometry detection for the analysis of microRNA biomarkers

Jeanneth Vasconez, Roger Peró Gascón (UGent) , Estela Gimenez and Fernando Benavente

(2020) TALANTA. 219.

Targeted profiling of protein phosphorylation in plants

Increasing the overall proteome coverage by combining protein digestion by Tryp-N and trypsin

A decoupled Virotrap approach to study the interactomes of N-terminal proteoforms

Methods in phytohormone detection and quantification: 2022

Proteomics standards initiative at twenty years : current activities and future work

Identification of new telomere- and telomerase-associated autoantigens in systemic sclerosis

Cataloguing protein complexes in planta using TurboID-catalyzed proximity labeling

Toward an integrated machine learning model of a proteomics experiment

Evaluation of alternative gas chromatographic and mass spectrometric behaviour of trimethylsilyl-derivatives of non-hydrolysed sulfated anabolic steroids

Universal at-line microbial fermentation monitoring through advances in rapid ambient ionisation mass spectrometry-based metabolomics

Recent advances in high-throughput biofluid metabotyping by direct infusion and ambient ionization mass spectrometry

Quality control for the target decoy approach for peptide identification

Proteomic comparison between non-purified cerebrospinal fluid and cerebrospinal fluid-derived extracellular vesicles from patients with Alzheimer's, Parkinson's and Lewy body dementia

Virotrap: Trapping Protein Complexes in Virus-Like Particles

A bioanalytical screening method for Enterococcus faecalis RNPP-type quorum sensing peptides in murine feces

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Characterization of RBPome in oxidative stress conditions

Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samples

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

It is never too late for a cocktail : development and analytical characterization of fixed-dose antibody combinations

Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics

A review of sample preparation for purification of microRNAs and analysis by mass spectrometry methods

Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

A comprehensive evaluation of consensus spectrum generation methods in proteomics

On-line immobilized enzyme microreactor capillary zone electrophoresis-mass spectrometry for peptide mapping

Proteomic comparison of three wild-type pseudorabies virus strains and the attenuated bartha strain reveals reduced incorporation of several tegument proteins in bartha virions

New applications of advanced instrumental techniques for the characterization of food allergenic proteins

High throughput analytical report writing in R : a case study of validating an LC-MS method for the quantification of amoxicillin in human plasma

Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)

Proteome profiling of RNF213 depleted cells reveals nitric oxide regulator DDAH1 antilisterial activity

Add mass spectrometry to the pandemic toolbox

Identification of non-canonical translation products in C. elegans using tandem mass spectrometry

Doping control analysis of small peptides : a decade of progress

Hepatic cytochrome P450 abundance and activity in the developing and adult Gottingen Minipig : Pivotal data for PBPK modeling

Histone sample preparation for bottom-up mass spectrometry : a roadmap to informed decisions

Mass spectrometry-based clinical proteomics : a revival

Proteomics mapping of the ISGylation landscape in innate immunity

Sample preparation free mass spectrometry using laser-assisted rapid evaporative ionization mass spectrometry : applications to microbiology, metabolic biofluid phenotyping, and food authenticity

Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Development of methods for Mg, Sr and Pb isotopic analysis of crude oil by MC-ICP-MS : addressing the challenges of sample decomposition

Rapid screening of diverse biotransformations for enzyme evolution

Surface coat proteins of the potato cyst nematode, Globodera rostochiensis

Development and application of an analytical method to quantify odour removal in plastic waste recycling processes

Urinary detection of rapid‐acting insulin analogues in healthy humans

Characterization of the new isotopic reference materials IRMM-524A and ERM-AE143 for Fe and Mg isotopic analysis of geological and biological samples

Three decades of listeriology through the prism of technological advances

Comparative study of concatemer efficiency as an isotope-labelled internal standard for allergen quantification

Next-generation protein analysis in the pathology department

Comparison of capillary electrophoresis and zwitterionic-hydrophilic interaction capillary liquid chromatography with ultraviolet and mass spectrometry detection for the analysis of microRNA biomarkers