Schäfer P, Helm S, Köhler D, Agne B, Baginsky S.
Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes.
PLoS One. 2019 Mar 13;14(3):e0213364. doi:10.1371/journal.pone.0213364. eCollection 2019. PubMed PMID: 30865669; PubMed Central PMCID: PMC6415892.


Rödiger A, Baginsky S.
Tailored Use of Targeted Proteomics in Plant-SpecificApplications.
Front Plant Sci. 2018 Aug 17;9:1204. doi: 10.3389/fpls.2018.01204. eCollection 2018. PubMed PMID: 30174680; PubMed Central PMCID: PMC6107752.

Frank J, Happeck R, Meier B, Hoang MTT, Stribny J, Hause G, Ding H, Morsomme P, Baginsky S, Peiter E.
Chloroplast-localized BICAT proteins shape stromal calcium signals and are required for efficient photosynthesis.
New Phytol. 2019 Jan;221(2):866-880. doi: 10.1111/nph.15407. Epub 2018 Aug 31. PubMed PMID:30169890.

Hempel F, Stenzel I, Heilmann M, Krishnamoorthy P, Menzel W, Golbik R, Helm S, Dobritzsch D, Baginsky S, Lee J, Hoehenwarter W, Heilmann I.
MAPKs Influence Pollen Tube Growth by Controlling the Formation of Phosphatidylinositol 4,5-Bisphosphate in an Apical Plasma Membrane Domain.
Plant Cell. 2017 Dec;29(12):3030-3050. doi: 10.1105/tpc.17.00543. Epub 2017 Nov 22. PubMed PMID:29167320; PubMed Central PMCID: PMC5757277.

Helm S, Baginsky S.
MSE for Label-Free Absolute Protein Quantification in Complex Proteomes.
Methods Mol Biol. 2018;1696:235-247. doi:10.1007/978-1-4939-7411-5_16. PubMed PMID: 29086408.


Wiesemann N, Bütof L, Herzberg M, Hause G, Berthold L, Etschmann B, Brugger J, Martinez-Criado G, Dobritzsch D, Baginsky S, Reith F
Synergistic toxicity of copper and gold compounds in Cupriavidus metallidurans
Nies DH. Appl Environ Microbiol. 2017 01679-17

Schönberg, A., Rödiger, A., Mehwald, W., Galonska, J., Christ, G., Helm, S., Thieme, D., Majovsky, P., Hoehenwarter, W., Baginsky, S.
Identification of STN7/STN8 kinase targets reveals connections between electron transport, metabolism and gene expression
Plant J. 2017 Jun;90(6):1176-1186. doi: 10.1111/tpj.13536. Epub 2017 Apr 21. PubMed PMID: 28295753.

Zufferey, M., Montandon, C., Douet, V., Demarsy, E., Agne, B., Baginsky, S., Kessler, F.
The Novel Chloroplast Outer Membrane Kinase KOC1 Is a Required Component of the Plastid Protein Import Machinery
J Biol Chem. 2017 Mar 10. pii: jbc.M117.776468

Agne, B., Köhler, D., Baginsky, S.
Protein import-independent functions of Tic56, a component of the 1-MDa translocase at the inner chloroplast envelope membrane
Plant Signal Behav. 2017;12(3):e1284726.


Köhler, D., Helm, S.,Agne, B., Baginsky, S.
Importance of Translocon Subunit Tic56 for rRNA Processing and Chloroplast Ribosome Assembly
Plant Physiol. 2016; 172(4):2429-2444

Richter, A.S., Gartmann, H., Fechler, M., Rödiger, A., Baginsky, S., Grimm B.
Identification of four plastid-localized protein kinases
FEBS Lett. 2016; 590(12):1749-56.

Baginsky, S.
Protein phosphorylation in chloroplasts – a survey of phosphorylation targets
J Exp Bot. 2016; 67 (13): 3873-3882


Köhler, D., Dobritzsch, D., Hoehenwarter,W., Helm, S., Steiner, J.M., Baginsky, S.
Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation.
Front Plant Sci. 2015; 6:559

Lu, Q., Helm, S., Rödiger, A., Baginsky, S.
On the extent of tyrosine phosphorylation in chloroplasts
Plant Physiol. 2015;169(2):996-1000

Schönberg, A., Baginsky, S.
The Peptide Microarray ChloroPhos1.0: A Screening Tool for the Identification of Arabidopsis thaliana Chloroplast Protein Kinase Substrates
Methods Mol Biol. 2015; 1306:147-57

Köhler D, Montandon C, Hause G, Majovsky P, Kessler F, Baginsky S, Agne B.
Characterization of chloroplast protein import without Tic56, a component of the 1-MDa TIC translocon
Plant Physiol. 2015 Jan 14. pii: pp.114.255562.


Betterle N, Ballottari M, Baginsky S, Bassi R.
High Light-Dependent Phosphorylation of Photosystem II Inner Antenna CP29 in Monocots Is STN7 Independent and Enhances Nonphotochemical Quenching.
Plant Physiol. 2015 Feb;167(2):457-71

Lu Q, Ding S, Reiland S, Rödiger A, Roschitzki B, Xue P, Gruissem W, Lu C, Baginsky S.
Identification and characterization of chloroplast casein kinase II from Oryza sativa (rice)
J Exp Bot. 2015 Jan;66(1):175-87

Joaquín-Ramos, A., Huerta-Ocampo, JÁ., Barrera-Pacheco, A., De León-Rodríguez, A., Baginsky, S., Barba de la Rosa, AP.,
Comparative proteomic analysis of amaranth mesophyll and bundle sheath chloroplasts and their adaptation to salt stress.
J Plant Physiol. 2014; 171(15):1423-35

Herzberg, M., Dobritzsch, D., Helm, S., Baginsky, S., Nies, D.H.
The zinc repository of Cupriavidus metallidurans
Metallomics, 2014;6(11):2157-2165

Schönberg A, Bergner E, Helm S, Agne B, Dünschede B, Schünemann D, Schutkowski M, Baginsky S.
The peptide microarray "ChloroPhos1.0" identifies new phosphorylation targets of plastid casein kinase II (pCKII) in Arabidopsis thaliana.
PLoS One. 2014 Oct 8;9(10):e108344. doi: 10.1371/journal.pone.0108344. eCollection 2014. PubMed PMID: 25295873; PubMed Central PMCID: PMC4189921.

Joaquín-Ramos, A., Huerta-Ocampo, JÁ., Barrera-Pacheco, A., De León-Rodríguez, A., Baginsky, S., Barba de la Rosa, AP.
Comparative proteomic analysis of amaranth mesophyll and bundle sheath chloroplasts and their adaptation to salt stress.
J Plant Physiol. 2014; 171(15):1423-35

Grimmer, J., Rödiger, A., Hoehenwarter, W., Helm, S., Baginsky, S.
The RNA-binding protein RNP29 is an unusual Toc159 transport substrate
Front Plant Sci. 2014;5:258

Helm, S., Dobritzsch, D., Rödiger, A.,  Agne, B., Baginsky, S.
Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome
J Proteomics. 2014;98:79-89

Rödiger, A., Agne, B., Baerenfaller, K., Baginsky, S.,
Arabidopsis proteomics: a simple and standardizable workflow for quantitative proteome characterization.
Methods Mol Biol. 2014;1072:275-88


Helm S, Dobritzsch D, Rödiger A, Agne B, Baginsky S.
Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome.
J Proteomics. 2014 Feb 26;98:79-89. doi:10.1016/j.jprot.2013.12.007. Epub 2013 Dec 18. PubMed PMID: 24361574.


Schönberg, A., Baginsky, S.
Signal integration by chloroplast phosphorylation networks: an update
Front Plant Science, 3, p.256

Motohashi, R., Rödiger, A., Agne,B., Baerenfaller, K., Baginsky, S.,
Common and specific protein accumulation patterns in different albino/pale-green mutants reveals regulon organization at the proteome level
Plant Physiology, 160(4), p.2189

Baerenfaller, K., Massonnet, C., Walsh, S., Baginsky, S., Bühlmann, P., Hennig, L., Hirsch-Hoffmann, M., Howell, K.A., Kahlau, S., Radziejwoski, A., Russenberger, D., Rutishauser, D., Small, I., Stekhoven, D., Sulpice, R., Svozil, J., Wuyts, N., Stitt, M., Hilson, P., Granier, C., Gruissem, W.
Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit
Molecular Systems Biology, 8, p.606


Bischof, S., Baerenfaller, K., Wildhaber, T., Troesch, R., Vidi, P.-A., Roschitzki, B., Hirsch-Hoffmann, M. Hennig, L., Kessler, F., Gruissem, W., Baginsky, S.
Plastid Proteome Assembly without Toc159: Photosynthetic Protein Import and Accumulation of N-Acetylated Plastid Precursor Proteins
Plant Cell, 23(11), p. 3911-3928.

Endler A, Baginsky S.
Use of phosphoproteomics to study posttranslational protein modifications in Arabidopsis chloroplasts.
Methods Mol Biol.2011;775:283-96. doi: 10.1007/978-1-61779-237-3_15. PubMed PMID: 21863449.

Reiland, S., Finazzi, G., Endler, A., Willig, A., Baerenfaller, K., Grossmann, J., Gerrits, B., Rutishauser, D., Gruissem, W., Rochaix, J.-D. & Baginsky, S.
Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF).
Proceedings of the National Academy of Sciences.

Gfeller, A., Baerenfaller, K., Loscos, J., Chételat, A., Baginsky, S. & Farmer, E.
Jasmonate controls polypeptide patterning in undamaged tissue in wounded Arabidopsis leaves.
Plant Physiology.

Reiland, S., Grossmann, J., Baerenfaller, K., Gehrig, P., Nunes‐Nesi, A., Fernie, A.R., Gruissem, W. & Baginsky, S.
Integrated proteome and metabolite analysis of the de‐etiolation process in plastids from rice (Oryza sativa L.).

van Wijk, K.J. & Baginsky, S.
Plastid Proteomics in Higher Plants: Current State and Future Goals.
Plant Physiology, 155(4), p.1578 -1588.

Baerenfaller, K., Hirsch-Hoffmann, M., Svozil, J., Hull, R., Russenberger, D., Bischof, S., Lu, Q., Gruissem, W. & Baginsky, S.
pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana.
Integrative Biology, 3(3), p.225.

Infanger, S., Bischof, S., Hiltbrunner, A., Agne, B., Baginsky, S. & Kessler, F.
The Chloroplast Import Receptor Toc90 Partially Restores the Accumulation of Toc159 Client Proteins in the Arabidopsis thaliana ppi2 Mutant.
Molecular Plant, 4, p.252-63.


Joshi, H.J., Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W., Baginsky, S., Schmidt, R., Shulze, W.X., Sun, Q., van Wijk, K.J., Egelhofer, V., Wienkoop, S., Weckwerth, W., Bruley, C., Rolland, N., Toyoda, T., Nakagami, H., Jones, A.M.E., Briggs, S.P., Castleden, I., Tanz, S.K., Millar, A.H. & Heazlewood, J.L.
MASCP Gator: An aggregation portal for the visualization of Arabidopsis proteomics data.
Plant Physiology, 2011 Jan;155(1):259-70. doi: 10.1104/pp.110.168195. Epub 2010 Nov 12. PubMed PMID:21075962; PubMed Central PMCID: PMC3075751.

Wienkoop, S., Baginsky, S. & Weckwerth, W.
Arabidopsis thaliana as a model organism for plant proteome research.
Journal of Proteomics, 73(11), p.2239-2248.

Agne, B., Andres, C., Montandon, C., Christ, B., Ertan, A., Jung, F., Infanger, S., Bischof, S., Baginsky, S. & Kessler, F.
The Acidic A-Domain of Arabidopsis Toc159 Occurs as a Hyperphosphorylated Protein.
Plant Physiol., 153(3), 1016-1030.


Baginsky, S., Hennig, L., Zimmermann, P. & Gruissem, W.
Gene Expression Analysis, Proteomics, and Network Discovery.
Plant Physiol., 152(2), 402-410.

Baginsky S, Gruissem W.
The chloroplast kinase network: new insights from large-scale phosphoproteome profiling.
Mol Plant. 2009 Nov;2(6):1141-53. doi:10.1093/mp/ssp058. Epub 2009 Aug 10. Review. PubMed PMID: 19995723.

Reiland, S., Messerli, G., Baerenfaller, K., Gerrits, B., Endler, A., Grossmann, J., Gruissem, W. & Baginsky, S.
Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks.
Plant Physiol., 150(2), 889-903.

Endler, A., Reiland, S., Gerrits, B., Schmidt, U.G., Baginsky, S. & Martinoia, E.,
In vivo phosphorylation sites of barley tonoplast proteins identified by a phosphoproteomic approach.
PROTEOMICS, 9(2), 310-321.

Baginsky, S.
Plant proteomics: Concepts, applications, and novel strategies for data interpretation.
Mass Spectrometry Reviews, 28(1), 93-120.


Weckwerth, W., Baginsky, S., van Wijk, K., Heazlewood, J.L. & Millar, H.,
The Multinational Arabidopsis Steering Subcommittee for Proteomics Assembles the Largest Proteome Database Resource for Plant Systems Biology.
Journal of Proteome Research, 7(10), 4209-4210.

Baerenfaller, K., Grossmann, J., Grobei, M.A., Hull, R., Hirsch-Hoffmann, M., Yalovsky, S., Zimmermann, P., Grossniklaus, U., Gruissem, W. & Baginsky, S.
Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics.
Science, 320(5878), 938-941.


Grossmann, J., Fischer, B., Baerenfaller, K., Owiti, J., Buhmann, J.M., Gruissem, W. & Baginsky, S.
A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments.
PROTEOMICS, 7(23), 4245-4254.

Roos, F.F., Jacob, R., Grossmann, J., Fischer, B., Buhmann, J.M., Gruissem, W., Baginsky, S. & Widmayer, P.,
PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.
Bioinformatics, 23(22), 3016-3023.

Schmidt, U.G., Endler, A., Schelbert, S., Brunner, A., Schnell, M., Neuhaus, H.E., Marty-Mazars, D., Marty, F., Baginsky, S. & Martinoia, E.
Novel Tonoplast Transporters Identified Using a Proteomic Approach with Vacuoles Isolated from Cauliflower Buds.
Plant Physiol., 145(1), 216-229.

Baginsky, S., Grossmann, J. & Gruissem, W.
Proteome Analysis of Chloroplast mRNA Processing and Degradation.
Journal of Proteome Research, 6(2), 809-820.


Kleffmann, T., von Zychlinski, A., Russenberger, D., Hirsch-Hoffmann, M., Gehrig, P., Gruissem, W. & Baginsky, S.
Proteome Dynamics during Plastid Differentiation in Rice.
Plant Physiol. , 143(2), 912-923.

Siddique, M.A., Grossmann, J., Gruissem, W. & Baginsky, S.
Proteome Analysis of Bell Pepper (Capsicum annuum L.) Chromoplasts.
Plant Cell Physiol., 47(12), 1663-1673.

Fischer, B., Grossmann, J., Roth, V., Gruissem, W., Baginsky, S. & Buhmann, J.M.,
Semi-supervised LC/MS alignment for differential proteomics.
Bioinformatics , 22(14), e132-140.

Endler, A., Meyer, S., Schelbert, S., Schneider, T., Weschke, W., Peters, S.W., Keller, F., Baginsky, S., Martinoia, E. & Schmidt, U.G.
Identification of a Vacuolar Sucrose Transporter in Barley and Arabidopsis Mesophyll Cells by a Tonoplast Proteomic Approach.
Plant Physiol. , 141(1), 196-207.

Baginsky, S. & Gruissem, W.
Arabidopsis thaliana proteomics: from proteome to genome.
J. Exp. Bot. , 57(7), 1485-1491.

Kleffmann, T., Hirsch-Hoffmann, M., Gruissem, W. & Baginsky, S.,
plprot: A Comprehensive Proteome Database for Different Plastid Types.
Plant Cell Physiol ., 47(3), 432-436.

Vidi, P., Kanwischer, M., Baginsky, S., Austin, J.R., Csucs, G., Dörmann, P., Kessler, F. & Bréhélin, C.,
Tocopherol Cyclase (VTE1) Localization and Vitamin E Accumulation in Chloroplast Plastoglobule Lipoprotein Particles.
Journal of Biological Chemistry , 281(16), 11225 -11234.

Nesvizhskii, A.I., Roos, F.F., Grossmann, J., Vogelzang, M., Eddes, J.S., Gruissem, W., Baginsky, S. & Aebersold, R.,
Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data.
Molecular & Cellular Proteomics , 5(4), 652-670.


Fischer, B., Roth, V., Roos, F., Grossmann, J., Baginsky, S., Widmayer, P., Gruissem, W. & Buhmann, J.M.
NovoHMM:  A Hidden Markov Model for de Novo Peptide Sequencing.
Analytical Chemistry, 77(22), 7265-7273.

Grossmann, J., Roos, F.F., Cieliebak, M., Lipták, Z., Mathis, L.K., Müller, M., Gruissem, W. & Baginsky, S.
AUDENS:  A Tool for Automated Peptide de Novo Sequencing.
Journal of Proteome Research, 4(5), 1768-1774.

Mayer, D., Baginsky, S. & Schwemmle, M.,
Isolation of viral ribonucleoprotein complexes from infected cells by tandem affinity purification.
PROTEOMICS, 5(17), 4483-4487.

Zychlinski, A., Kleffmann, T., Krishnamurthy, N., Sjölander, K., Baginsky, S. & Gruissem, W.,
Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions. Mol Cell Proteomics.
Molecular & Cellular Proteomics, 4(8), 1072-1084.

Baginsky, S., Kleffmann, T., von Zychlinski, A. & Gruissem, W.
Analysis of Shotgun Proteomics and RNA Profiling Data from Arabidopsis thaliana Chloroplasts.
Journal of Proteome Research , 4(2), 637-640.