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Article

Combining Data Independent Acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification.
Welter, A.S., Gerwien, M., Kerridge, R., Alp, K.M., Mertins, P. and Selbach, M.
Molecular & Cellular Proteomics 23 (10): 100839. October 2024

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics.
Makhmut, A., Qin, D., Hartlmayr, D., Seth, A. and Coscia, F.
Molecular & Cellular Proteomics 23 (5): 100750. May 2024

What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome?
Prensner, J.R., Abelin, J.G., Kok, L.W., Clauser, K.R., Mudge, J.M., Ruiz-Orera, J., Bassani-Sternberg, M., Moritz, R.L., Deutsch, E.W. and van Heesch, S.
Molecular & Cellular Proteomics 22 (9): 100631. September 2023

A universal peptide matrix interactomics approach to disclose motif dependent protein binding.
Ramberger, E., Suarez-Artiles, L., Perez-Hernandez, D., Haji, M., Popp, O., Reimer, U., Leutz, A., Dittmar, G. and Mertins, P.
Molecular & Cellular Proteomics 20 : 100135. 13 August 2021

TMT labeling for the masses: a robust and cost-efficient, in-solution labeling approach.
Zecha, J., Satpathy, S., Kanashova, T., Avanessian, S.C., Kane, M.H., Clauser, K.R., Mertins, P., Carr, S.A. and Kuster, B.
Molecular & Cellular Proteomics 18 (7): 1468-1478. 1 July 2019

A curated resource for phosphosite-specific signature analysis.
Krug, K., Mertins, P., Zhang, B., Hornbeck, P., Raju, R., Ahmad, R., Szucs, M., Mundt, F., Forestier, D., Jane-Valbuena, J., Keshishian, H., Gillette, M.A., Tamayo, P., Mesirov, J.P., Jaffe, J.D., Carr, S.A. and Mani, D.R.
Molecular & Cellular Proteomics 18 (3): 576-593. 1 March 2019

Quantitative proteomic approach identifies Vpr binding protein as novel host factor supporting influenza A virus infections in human cells.
Sadewasser, A., Paki, K., Eichelbaum, K., Bogdanow, B., Saenger, S., Budt, M., Lesch, M., Hinz, K.P., Herrmann, A., Meyer, T.F., Karlas, A., Selbach, M. and Wolff, T.
Molecular & Cellular Proteomics 16 (5): 728-742. 1 May 2017

Quantitative GTPase affinity purification identifies Rho family protein interaction partners.
Paul, F., Zauber, H., von Berg, L., Rocks, O., Daumke, O. and Selbach, M.
Molecular & Cellular Proteomics 16 (1): 73-85. 1 January 2017

Proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction.
Wang, J., Ma, Z., Carr, S.A., Mertins, P., Zhang, H., Zhang, Z., Chan, D.W., Ellis, M.J.C., Townsend, R.R., Smith, R.D., McDermott, J.E., Chen, X., Paulovich, A.G., Boja, E.S., Mesri, M., Kinsinger, C.R., Rodriguez, H., Rodland, K.D., Liebler, D.C. and Zhang, B.
Molecular & Cellular Proteomics 16 (1): 121-134. 1 January 2017

Systematic errors in peptide and protein identification and quantification by modified peptides.
Bogdanow, B., Zauber, H. and Selbach, M.
Molecular & Cellular Proteomics 15 (8): 2791-2801. 1 August 2016

In vivo interaction proteomics in Caenorhabditis elegans embryos provides new insights into P granule dynamics.
Chen, J.X., Cipriani, P.G., Mecenas, D., Polanowska, J., Piano, F., Gunsalus, K.C. and Selbach, M.
Molecular & Cellular Proteomics 15 (5): 1642-1657. 1 May 2016

An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer.
Ruggles, K.V., Tang, Z., Wang, X., Grover, H., Askenazi, M., Teubl, J., Cao, S., McLellan, M.D., Clauser, K.R., Tabb, D.L., Mertins, P., Slebos, R., Erdmann-Gilmore, P., Li, S., Gunawardena, H.P., Xie, L., Liu, T., Zhou, J.Y., Sun, S., Hoadley, K.A., Perou, C.M., Chen, X., Davies, S.R., Maher, C.A., Kinsinger, C.R., Rodland, K.D., Zhang, H., Zhang, Z., Ding, L., Townsend, R.R., Rodriguez, H., Chan, D., Smith, R.D., Liebler, D.C., Carr, S.A., Payne, S., Ellis, M.J. and Fenyö, D.
Molecular & Cellular Proteomics 15 (3): 1060-1071. 1 March 2016

Multiplexed, quantitative workflow for sensitive biomarker discovery in plasma yields novel candidates for early myocardial injury.
Keshishian, H., Burgess, M.W., Gillette, M.A., Mertins, P., Clauser, K.R., Mani, D.R., Kuhn, E.W., Farrell, L.A., Gerszten, R.E. and Carr, S.A.
Molecular & Cellular Proteomics 14 (9): 2375-2393. 1 September 2015

Deep, quantitative coverage of the lysine acetylome using novel anti-acetyl-lysine antibodies and an optimized proteomic workflow.
Svinkina, T., Gu, H., Silva, J.C., Mertins, P., Qiao, J., Fereshetian, S., Jaffe, J.D., Kuhn, E., Udeshi, N.D. and Carr, S.A.
Molecular & Cellular Proteomics 14 (9): 2429-2440. 1 September 2015

Cytoskeletal components define protein location to membrane microdomains.
Szymanski, W.G., Zauber, H., Erban, A., Wu, X.N. and Schulze, W.X.
Molecular & Cellular Proteomics 14 (9): 2493-2509. September 2015

Functional proteomic analysis of repressive histone methyltransferase complexes reveals ZNF518B as a G9A regulator.
Maier, V.K., Feeney, C.M., Taylor, J.E., Creech, A.L., Qiao, J.W., Szanto, A., Das, P.P., Chevrier, N., Cifuentes-Rojas, C., Orkin, S.H., Carr, S.A., Jaffe, J.D., Mertins, P. and Lee, J.T.
Molecular & Cellular Proteomics 14 (6): 1435-1446. 1 June 2015

Quantitative proteomics reveals dynamic interaction of c-Jun N-terminal kinase (JNK) with RNA transport granule proteins splicing factor proline- and glutamine-rich (Sfpq) and non-POU domain-containing octamer-binding protein (Nono) during neuronal differentiation.
Sury, M.D., McShane, E., Hernandez-Miranda, L.R., Birchmeier, C. and Selbach, M.
Molecular & Cellular Proteomics 14 (1): 50-65. 1 January 2015

Using in vivo-biotinylated ubiquitin to describe a mitotic exit ubiquitome from human cells.
Min, M., Mayor, U., Dittmar, G. and Lindon, C.
Molecular & Cellular Proteomics 13 (9): 2411-2425. September 2014

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.
Mertins, P., Yang, F., Liu, T., Mani, D.R., Petyuk, V.A., Gillette, M.A., Clauser, K.R., Qiao, J.W., Gritsenko, M.A., Moore, R.J., Levine, D.A., Townsend, R., Erdmann-Gilmore, P., Snider, J.E., Davies, S.R., Ruggles, K.V., Fenyo, D., Kitchens, R.T., Li, S., Olvera, N., Dao, F., Rodriguez, H., Chan, D.W., Liebler, D., White, F., Rodland, K.D., Mills, G.B., Smith, R.D., Paulovich, A.G., Ellis, M. and Carr, S.A.
Molecular & Cellular Proteomics 13 (7): 1690-1704. 1 July 2014

Identification of importin alpha 7 specific transport cargoes using a proteomic screening approach.
Hügel, S., Depping, R., Dittmar, G., Rother, F., Cabot, R., Sury, M.D., Hartmann, E. and Bader, M.
Molecular & Cellular Proteomics 13 (5): 1286-1298. 1 May 2014

Proteomic and functional consequences of hexokinase deficiency in glucose-repressible Kluyveromyces lactis.
Mates, N., Kettner, K., Heidenreich, F., Pursche, T., Migotti, R., Kahlert, G., Kuhlisch, E., Breunig, K.D., Schellenberger, W., Dittmar, G., Hoflack, B. and Kriegel, T.M.
Molecular & Cellular Proteomics 13 (3): 860-875. 1 March 2014

Protein sets define disease states and predict in vivo effects of drug treatment.
Meierhofer, D., Weidner, C., Hartmann, L., Mayr, J.A., Han, C.T., Schroeder, F.C. and Sauer, S.
Molecular & Cellular Proteomics 12 (7): 1965-1979. 1 July 2013

Argonaute2 regulates the pancreatic β-cell secretome.
Tattikota, S.G., Sury, M.D., Rathjen, T., Wessels, H.H., Pandey, A.K., You, X., Becker, C., Chen, W., Selbach, M. and Poy, M.N.
Molecular & Cellular Proteomics 12 (5): 1214-1225. May 2013

Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
Udeshi, N.D., Svinkina, T., Mertins, P., Kuhn, E., Mani, D.R., Qiao, J.W. and Carr, S.A.
Molecular & Cellular Proteomics 12 (3): 825-831. 1 March 2013

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.
Mertins, P., Udeshi, N.D., Clauser, K.R., Mani, D.R., Patel, J., Ong, S.E., Jaffe, J.D. and Carr, S.A.
Molecular & Cellular Proteomics 11 (6): M111.014423. 1 June 2012

Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease.
Moeller, A., Xie, S.Q., Hosp, F., Lang, B., Phatnani, H.P., James, S., Ramirez, F., Collin, G.B., Naggert, J.K., Babu, M.M., Greenleaf, A.L., Selbach, M. and Pombo, A.
Molecular & Cellular Proteomics 11 (6): M111.011767. June 2012

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Udeshi, N.D., Mani, D.R., Eisenhaure, T., Mertins, P., Jaffe, J.D., Clauser, K.R., Hacohen, N. and Carr, S.A.
Molecular & Cellular Proteomics 11 (5): 148-159. 1 May 2012

The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.
Naba, A., Clauser, K.R., Hoersch, S., Liu, H., Carr, S.A. and Hynes, R.O.
Molecular & Cellular Proteomics 11 (4): M111.014647. 1 April 2012

Large-scale de novo prediction of physical protein-protein association.
Elefsinioti, A., Sarac, O.S., Hegele, A., Plake, C., Hubner, N.C., Poser, I., Sarov, M., Hyman, A., Mann, M., Schroeder, M., Stelzl, U. and Beyer, A.
Molecular & Cellular Proteomics 10 (11): M111.010629. November 2011

Identification of increased amounts of eppin protein complex components in sperm cells of diabetic and obese individuals by difference gel electrophoresis.
Paasch, U., Heidenreich, F., Pursche, T., Kuhlisch, E., Kettner, K., Grunewald, S., Kratzsch, J., Dittmar, G., Glander, H.J., Hoflack, B. and Kriegel, T.M.
Molecular & Cellular Proteomics 10 (8): M110.007187. August 2011

The SILAC fly allows for accurate protein quantification in vivo.
Sury, M.D., Chen, J.X. and Selbach, M.
Molecular & Cellular Proteomics 9 (10): 2173-2183. October 2010

A large number of protein expression changes occur early in life and precede phenotype onset in a mouse model for huntington disease.
Zabel, C., Mao, L., Woodman, B., Rohe, M., Wacker, M.A., Klaere, Y., Koppelstaetter, A., Nebrich, G., Klein, O., Grams, S., Strand, A., Luthi-Carter, R., Hartl, D., Klose, J. and Bates, G.P.
Molecular & Cellular Proteomics 8 (4): 720-734. 1 April 2009

Investigation of protein-tyrosine phosphatase 1B function by quantitative proteomics.
Mertins, P., Eberl, H.C., Renkawitz, J., Olsen, J.V., Tremblay, M.L., Mann, M., Ullrich, A. and Daub, H.
Molecular & Cellular Proteomics 7 (9): 1763-1777. September 2008

Identification of the ligands of protein interaction domains through a functional approach.
Caratù, G., Allegra, D., Bimonte, M., Schiattarella, G.G., D'Ambrosio, C., Scaloni, A., Napolitano, M., Russo, T. and Zambrano, N.
Molecular & Cellular Proteomics 6 (2): 333-345. February 2007

Identification of VCP/p97, CHIP and amphiphysin II interaction partners using membrane-based human proteome arrays.
Grelle, G., Kostka, S., Otto, A., Kersten, B., Genser, K.F., Mueller, E.C., Waelter, S., Boeddrich, A., Stelzl, U., Haenig, C., Volkmer-Engert, R., Landgraf, C., Alberti, S., Hoehfeld, J., Stroedicke, M. and Wanker, E.E.
Molecular & Cellular Proteomics 5 (2): 234-244. 1 February 2006

High-throughput identification of potential Arabidopsis MAP kinases substrates.
Feilner, T., Hultschig, C., Lee, J., Meyer, S., Immink, R.G., Koenig, A., Possling, A., Seitz, H., Beveridge, A., Scheel, D., Cahill, D.J., Lehrach, H., Kreutzberger, J. and Kersten, B.
Molecular & Cellular Proteomics 4 (10): 1558-1568. 11 July 2005

Review

An introduction to advanced targeted acquisition methods.
van Bentum, M. and Selbach, M.
Molecular & Cellular Proteomics 20 : 100165. 18 October 2021

Peptide-based interaction proteomics.
Meyer, K. and Selbach, M.
Molecular & Cellular Proteomics 19 (7): 1070-1075. July 2020