Article

Identification of MHC ligands through allele-guided isolation combined with machine learning for improved MHC assignment using ARDisplay-I.
Mecklenbräuker, Shima, Skoczylas, Piotr, Biernat, Paweł ORCID: https://orcid.org/0000-0003-1482-9621, Zaghla, Badeel K.H.Q. ORCID: https://orcid.org/0009-0002-2675-8859, Atay, Bilge ORCID: https://orcid.org/0009-0008-6968-8858, Hossam, Mai, Król-Józaga, Bartłomiej ORCID: https://orcid.org/0000-0003-2526-0629, Jasiński, Maciej ORCID: https://orcid.org/0000-0001-6467-2752, Pienkowski, Victor Murcia ORCID: https://orcid.org/0000-0002-1383-8019, Sanecka-Duin, Anna ORCID: https://orcid.org/0000-0001-7684-2149, Popp, Oliver ORCID: https://orcid.org/0000-0001-6240-4666, Haji, Mohamed, Szatanek, Rafał, Mertins, Philipp ORCID: https://orcid.org/0000-0002-2245-528X, Kaczmarczyk, Jan ORCID: https://orcid.org/0000-0002-1629-3675, Keller, Ulrich ORCID: https://orcid.org/0000-0002-8485-1958, Blum, Agnieszka and Klatt, Martin G. ORCID: https://orcid.org/0000-0001-8703-7305
Molecular & Cellular Proteomics 25 (5): 101560. May 2026

An ultrasensitive spatial tissue proteomics workflow exceeding 100 proteomes per day.
Klingeberg, Melissa ORCID: https://orcid.org/0009-0002-4778-2874, Krisp, Christoph ORCID: https://orcid.org/0000-0002-4689-1967, Fritzsche, Sonja ORCID: https://orcid.org/0000-0003-3335-3534, Schallenberg, Simon, Hornburg, Daniel ORCID: https://orcid.org/0000-0002-6618-7774 and Coscia, Fabian ORCID: https://orcid.org/0000-0002-2244-5081
Molecular & Cellular Proteomics 25 (1): 101489. January 2026

Benchmarking of quantitative proteomics workflows for limited proteolysis mass spectrometry.
Koudelka, T. ORCID: https://orcid.org/0009-0008-2895-6051, Bassot, C. and Piazza, I. ORCID: https://orcid.org/0000-0001-5895-6134
Molecular & Cellular Proteomics 24 (4): 100945. April 2025

Combining Data Independent Acquisition with spike-in SILAC (DIA-SiS) improves proteome coverage and quantification.
Welter, A.S. ORCID: https://orcid.org/0009-0003-9846-3889, Gerwien, M. ORCID: https://orcid.org/0000-0002-2884-4155, Kerridge, R., Alp, K.M. ORCID: https://orcid.org/0000-0001-9919-9838, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Molecular & Cellular Proteomics 23 (10): 100839. October 2024

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics.
Makhmut, A. ORCID: https://orcid.org/0009-0009-6913-4289, Qin, D. ORCID: https://orcid.org/0000-0002-9730-4072, Hartlmayr, D., Seth, A. and Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081
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. ORCID: https://orcid.org/0000-0002-7024-636X, Abelin, J.G., Kok, L.W. ORCID: https://orcid.org/0009-0008-0841-2313, Clauser, K.R., Mudge, J.M. ORCID: https://orcid.org/0000-0003-4789-7495, Ruiz-Orera, J. ORCID: https://orcid.org/0000-0002-8317-0034, Bassani-Sternberg, M., Moritz, R.L. ORCID: https://orcid.org/0000-0002-3216-9447, Deutsch, E.W. and van Heesch, S. ORCID: https://orcid.org/0000-0001-9593-1980
Molecular & Cellular Proteomics 22 (9): 100631. September 2023

A universal peptide matrix interactomics approach to disclose motif dependent protein binding.
Ramberger, E. ORCID: https://orcid.org/0000-0003-2760-2696, Suarez-Artiles, L. ORCID: https://orcid.org/0000-0001-7991-5446, Perez-Hernandez, D. ORCID: https://orcid.org/0000-0003-0266-9050, Haji, M., Popp, O. ORCID: https://orcid.org/0000-0001-6240-4666, Reimer, U. ORCID: https://orcid.org/0000-0002-3375-6889, Leutz, A. ORCID: https://orcid.org/0000-0001-8259-927X, Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623 and Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X
Molecular & Cellular Proteomics 20 : 100135. 13 August 2021

TMT labeling for the masses: a robust and cost-efficient, in-solution labeling approach.
Zecha, J. ORCID: https://orcid.org/0000-0002-8767-6294, Satpathy, S., Kanashova, T., Avanessian, S.C., Kane, M.H., Clauser, K.R., Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0001-9845-1210, 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. ORCID: https://orcid.org/0000-0002-2402-6323, Eichelbaum, K., Bogdanow, B. ORCID: https://orcid.org/0000-0002-9634-7353, Saenger, S., Budt, M., Lesch, M., Hinz, K.P., Herrmann, A., Meyer, T.F., Karlas, A., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Wolff, T. ORCID: https://orcid.org/0000-0001-7688-236X
Molecular & Cellular Proteomics 16 (5): 728-742. 1 May 2017

Quantitative GTPase affinity purification identifies Rho family protein interaction partners.
Paul, F. ORCID: https://orcid.org/0000-0001-5181-3122, Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, von Berg, L., Rocks, O. ORCID: https://orcid.org/0000-0001-6349-9193, Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0003-2595-1147 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
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. ORCID: https://orcid.org/0000-0002-3671-553X, Cipriani, P.G., Mecenas, D., Polanowska, J., Piano, F., Gunsalus, K.C. and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0003-2595-1147, 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. ORCID: https://orcid.org/0000-0002-2245-528X 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. ORCID: https://orcid.org/0000-0002-7806-2063, Hernandez-Miranda, L.R. ORCID: https://orcid.org/0000-0002-0498-708X, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
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. ORCID: https://orcid.org/0000-0003-3647-8623 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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0003-3647-8623, Rother, F. ORCID: https://orcid.org/0000-0002-4417-2192, Cabot, R., Sury, M.D., Hartmann, E. and Bader, M. ORCID: https://orcid.org/0000-0003-4780-4164
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. ORCID: https://orcid.org/0000-0001-7183-1424, Kahlert, G., Kuhlisch, E., Breunig, K.D., Schellenberger, W., Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, 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. ORCID: https://orcid.org/0000-0002-4794-3693
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. ORCID: https://orcid.org/0000-0001-5551-404X, Pandey, A.K. ORCID: https://orcid.org/0000-0002-8886-1694, You, X., Becker, C., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Poy, M.N. ORCID: https://orcid.org/0000-0002-4904-2426
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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0003-2454-8751 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0003-2500-3585 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. ORCID: https://orcid.org/0000-0003-3647-8623, 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. ORCID: https://orcid.org/0000-0002-3671-553X and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
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. ORCID: https://orcid.org/0000-0002-2245-528X, 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. ORCID: https://orcid.org/0000-0002-7582-7171, 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. ORCID: https://orcid.org/0000-0001-9118-050X, Stelzl, U. ORCID: https://orcid.org/0000-0003-2500-3585, Haenig, C. ORCID: https://orcid.org/0000-0003-1973-7646, Volkmer-Engert, R., Landgraf, C., Alberti, S., Hoehfeld, J., Stroedicke, M. and Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630
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. ORCID: https://orcid.org/0000-0003-2454-8751
Molecular & Cellular Proteomics 20 : 100165. 18 October 2021

Peptide-based interaction proteomics.
Meyer, K. ORCID: https://orcid.org/0000-0002-8244-6887 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Molecular & Cellular Proteomics 19 (7): 1070-1075. July 2020