150 Class I and II neoantigen mapping in MSI-high colorectal cancer in needle biopsy size tissue samples

Autor: Roland Bruderer, Marco Tognetti, Lukas Reiter, Ilja E Shapiro, Luca Raess, Tikira Temu, Oliver M Bernhardt, Yuehan Feng, Jonathan Woodsmith

Publikováno v: Journal for ImmunoTherapy of Cancer, Vol 11, Iss Suppl 1 (2023)

Externí odkaz: https://doaj.org/article/a2bd5bb8daa8491185b5dd1be8228905

MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale

Autor: Devon Kohler, Mateusz Staniak, Tsung-Heng Tsai, Ting Huang, Nicholas Shulman, Oliver M. Bernhardt, Brendan X. MacLean, Alexey I. Nesvizhskii, Lukas Reiter, Eduard Sabido, Meena Choi, Olga Vitek

Publikováno v: Journal of Proteome Research. 22:1466-1482

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::0ea0acc1fc48452d28364cb6e2533067
https://doi.org/10.1021/acs.jproteome.2c00834

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance

Autor: Oliver Rinner, Ornella Cominetti, Jan Muntel, Jörg Hager, Charlotte Macron, Arne Astrup, Roland Bruderer, Wim H. M. Saris, Sebastian Müller, Loïc Dayon, Armand Valsesia, Jérôme Carayol, Oliver M. Bernhardt, Lukas Reiter, Tejas Gandhi

Publikováno v: Molecular & Cellular Proteomics, 18(6):ARTN RA118.001288, 1242-1254. American Society for Biochemistry and Molecular Biology, Inc.
Molecular & Cellular Proteomics : MCP
Bruderer, R, Muntel, J, Müller, S, Bernhardt, O M, Gandhi, T, Cominetti, O, Macron, C, Carayol, J, Rinner, O, Astrup, A, Saris, W H M, Hager, J, Valsesia, A, Dayon, L & Reiter, L 2019, ' Analysis of 1508 plasma samples by capillary-flow data-independent acquisition profiles proteomics of weight loss and maintenance ', Molecular and Cellular Proteomics, vol. 18, no. 6, pp. 1242-1254 . https://doi.org/10.1074/mcp.RA118.001288

We established a robust capillary-flow data-independent acquisition MS platform capable of measuring 31 plasma proteomes per day without the need of repeated acquisition of the same sample. We acquired 1508 samples of the DiOGenes study (multicentere

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e33a040f9603a6db3ea619215d48a53d
https://doi.org/10.1074/mcp.ra118.001288

MassIVE.quant: a community resource of quantitative mass spectrometry–based proteomics datasets

Autor: Ting Huang, Erik Verschueren, Yasset Perez-Riverol, Bernd Wollscheid, Ruth Hüttenhain, Jeremy Carver, Eduard Sabidó, Olga Vitek, Tom Dunkley, Guo Ci Teo, Oliver M. Bernhardt, Benjamin Pullman, Nuno Bandeira, Maria P. Pavlou, Lukas Reiter, Meena Choi, Cristina Chiva, Jan Muntel, Manuel Tzouros, Tsung-Heng Tsai, Alexey I. Nesvizhskii, Maik Müller, Sandra Goetze

Publikováno v: Nature Methods, 17 (10)
Nature methods
Nature Methods

MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational analysis tools. A branch structur

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d09560dbcf39706572c935962940d6e9
https://hdl.handle.net/20.500.11850/443807

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Autor: Tejas Gandhi, Ana Martinez-Val, Christian D. Kelstrup, Lynn Verbeke, Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Lukas Reiter, Alexander Hogrebe, Jesper V. Olsen

Publikováno v: Bekker-Jensen, D B, Bernhardt, O M, Hogrebe, A, Martinez-Val, A, Verbeke, L, Gandhi, T, Kelstrup, C D, Reiter, L & Olsen, J V 2020, ' Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries ', Nature Communications, vol. 11, no. 1, 787 . https://doi.org/10.1038/s41467-020-14609-1
Nature Communications
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)

Quantitative phosphoproteomics has transformed investigations of cell signaling, but it remains challenging to scale the technology for high-throughput analyses. Here we report a rapid and reproducible approach to analyze hundreds of phosphoproteomes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8e453d00707c07c35b75c671a2f2b94a
https://curis.ku.dk/portal/da/publications/rapid-and-sitespecific-deep-phosphoproteome-profiling-by-dataindependent-acquisition-without-the-need-for-spectral-libraries(c58b93b3-99f8-4b09-897a-9c279dc8d2c3).html