Proteomics Platform Publications

Below you will find the MPUSP publications, which include proteomics analyses carried out by members of the institute‘s proteomics platform (since 2019).

Preprints

1. Cornejo FA, Driller K, Ahmed-Begrich R, Schmidt K, Jahn M, Shanmuganathan V, Hahnke K, Kondrot F, Wulff TF, Rämisch S, Alagesan K, Charpentier E and Turgay K (2025) Targeting the translation machinery: The RNase Y specificity factor Y-complex coordinates ribosome degradation. bioRxiv. doi.org/10.1101/2025.06.27.661978
2. Rubinić M, Arias-Rojas A, Martinez KA, Klimek W, Paczia N, Alagesan K, Duneau D and Iatsenko I (2025) Sex differences in Drosophila intestinal metabolism contribute to sexually dimorphic infection outcome and alter gut pathogen virulence. bioRxiv. doi.org/10.1101/2025.05.22.655590 
3. Alagesan K, Ahmed-Begrich R and Charpentier E (2022) Improved N- and O-Glycopeptide identification using High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS). bioRxiv. doi.org/10.1101/2022.12.12.520086

 

Original Articles

1. Krause K, Franch Arroyo S, Ugolini M, Kueck T, Sullivan TJ, Gálvez EJC, Muenzner M, Goosmann C, Brinkmann V, Frese CK, Alagesan K, Vierbuchen T, Heine H, Resch U, Sander LE and Charpentier E (2025) Streptococcus pyogenes EVs induce the alternative inflammasome via caspase-4/-5 in human monocytes. EMBO Rep. 26(19):4847-4885. doi: 10.1038/s44319-025-00558-7
2. Ignatov D, Shanmuganathan V, Ahmed-Begrich R, Alagesan K, Hahnke K, Wang C, Krause K, Cornejo FA, Funke K, Erhardt M, Frese CK and Charpentier E (2025) RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria. Nat. Commun. 16(1):6262. doi: 10.1038/s41467-025-60687-4
3. Ajay Castro S, Passmore IJ, Ndeh D, Shaw HA, Ruda A, Burns K, Thomson S, Nagar R, Alagesan K, Reglinski M, Lucas K, Abouelhadid S, Schwarz-Linek U, Mawas F, Widmalm G, Wren BW and Dorfmueller HC (2025)Recombinant production platform for Group A Streptococcus glycoconjugate vaccines. NPJ Vaccines 10(1):16. doi: 10.1038/s41541-025-01068-2
4. Birk MS, Charpentier E and Frese CK (2021) Automated phosphopeptide enrichment for Gram-positive bacteria. J. Proteome Res. 20(10):4886-4892. doi: 10.1021/acs.jproteome.1c00364
5. Birk MS, Ahmed-Begrich R, Tran S, Elsholz AKW, Frese CK and Charpentier E (2021) Time-resolved proteome analysis of Listeria monocytogenes during infection reveals the role of the AAA+ chaperone ClpC for host cell adaptation. mSystems 6(4):e0021521. doi: 10.1128/mSystems.00215-21
6. Krishnamoorthy G, Kaiser P, Constant P, Abu Abed U, Schmid M, Frese CK, Brinkmann V, Daffé M and Kaufmann SHE (2021) Role of premycofactocin synthase in growth, microaerophilic adaptation, and metabolism of Mycobacterium tuberculosis. mBio 12(4):e0166521. doi: 10.1128/mBio.01665-21
7. Apel F, Andreeva L, Knackstedt LS, Streeck R, Frese CK, Goosmann C, Hopfner KP and Zychlinsky A (2021) The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps. Sci. Signal. 14(673):eaax7942. doi: 10.1126/scisignal.aax7942
8. Schnirch L, Nadler-Holly M, Siao SW, Frese CK, Viner R and Liu F (2020) Expanding the depth and sensitivity of cross-link identification by differential ion mobility using high-field asymmetric waveform ion mobility spectrometry. Anal. Chem. 92(15):10495-10503. doi: 10.1021/acs.analchem.0c01273
9. Schäfer H, Beckert B, Frese CK, Steinchen W, Nuss AM, Beckstette M, Hantke I, Driller K, Sudzinová P, Krásný L, Kaever V, Dersch P, Bange G, Wilson DN and Turgay K (2020) The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PLoS Genet. 16(3):e1008275. doi: 10.1371/journal.pgen.1008275

 

​​​​​​​Editorials, Opinions, Comments, Voices, Previews & Perspectives

1. Zhan X and Jungblut PR (2022) The comparison between 2DE-MS and bottom-up LC-MS demands high-end techniques for both technologies. Electrophoresis 43(11):1242-1245. doi: 10.1002/elps.202200036

 

​​​​​​​Review Articles

1. Zhan X, Li B, Zhan X, Schlüter H, Jungblut PR and Coorssen JR (2019) Innovating the concept and practice of two-dimensional gel electrophoresis in the analysis of proteomes at the proteoform level. Proteomes 7(4):36. doi: 10.3390/proteomes7040036

 

​​​​​​​​​​​​​​Book Chapters

1. Alagesan K and Charpentier E (2023) Systems-Wide Site-Specific Analysis of Glycoproteins. In: Gevaert, K. (eds) Mass Spectrometry-Based Proteomics. Methods in Molecular Biology, vol 2718. Humana, New York, NY. doi: 10.1007/978-1-0716-3457-8_9
2. Lisacek F, Alagesan K, Hayes C, Lippold S and de Haan N (2021) Bioinformatics in Immunoglobulin Glycosylation Analysis. In: Pezer, M. (eds) Antibody Glycosylation. Experientia Supplementum, vol 112. Springer, Cham. doi: 10.1007/978-3-030-76912-3_6
3. Alagesan K, Hoffmann M, Rapp E and Kolarich D (2020) Glycoproteomics Technologies in Glycobiotechnology. In: Rapp, E., Reichl, U. (eds) Advances in Glycobiotechnology. Advances in Biochemical Engineering/Biotechnology, vol 175. Springer, Cham. doi.org/10.1007/10_2020_144