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Comparing the extraction performance in mouse plasma of different biphasic methods for polar and nonpolar compounds.
Gutmann, F., Fritsche-Guenther, R., Dias, D.B. and Kirwan, J.A.
Journal of Proteome Research 23 (8): 2961-2969. 2 August 2024

In vitro Kinase-to-Phosphosite database (iKiP-DB) predicts kinase activity in phosphoproteomic datasets.
Mari, T., Mösbauer, K., Wyler, E., Landthaler, M., Drosten, C. and Selbach, M.
Journal of Proteome Research 21 (6): 1575-1587. 3 June 2022

TaxIt: an iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples.
Kuhring, M., Doellinger, J., Nitsche, A., Muth, T. and Renard, B.Y.
Journal of Proteome Research 19 (6): 2501-2510. 5 June 2020

Efficient application of de novo RNA assemblers for proteomics informed by transcriptomics.
Luge, T., Fischer, C. and Sauer, S.
Journal of Proteome Research 15 (10): 3938-3943. 7 October 2016

Minichromosome maintenance complex is a critical node in the miR-183 signaling network of MYCN-amplified neuroblastoma cells.
Lodrini, M., Poschmann, G., Schmidt, V., Wünschel, J., Dreidax, D., Witt, O., Höfer, T., Meyer, H.E., Stühler, K., Eggert, A. and Deubzer, H.E.
Journal of Proteome Research 15 (7): 2178-2186. 1 July 2016

Proteomics quality control : a quality control software for MaxQuant results.
Bielow, C., Mastrobuoni, G. and Kempa, S.
Journal of Proteome Research 15 (3): 777-787. 4 March 2016

Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts.
Tabb, D.L., Wang, X., Carr, S.A., Clauser, K.R., Mertins, P., Chambers, M.C., Holman, J.D., Wang, J., Zhang, B., Zimmerman, L.J., Chen, X., Gunawardena, H.P., Davies, S.R., Ellis, M.J.C., Li, S., Townsend, R.R., Boja, E.S., Ketchum, K.A., Kinsinger, C.R., Mesri, M., Rodriguez, H., Liu, T., Kim, S., McDermott, J.E., Payne, S.H., Petyuk, V.A., Rodland, K.D., Smith, R.D., Yang, F., Chan, D.W., Zhang, B., Zhang, H., Zhang, Z., Zhou, J.Y. and Liebler, D.C.
Journal of Proteome Research 15 (3): 691-706. 4 March 2016

Integrative analysis of transcriptomics, proteomics, and metabolomics data of white adipose and liver tissue of high-fat diet and rosiglitazone-treated insulin-resistant mice identified pathway alterations and molecular hubs.
Meierhofer, D., Weidner, C. and Sauer, S.
Journal of Proteome Research 13 (12): 5592-5602. 5 December 2014

Ubiquitin profiling in liver using a transgenic mouse with biotinylated ubiquitin.
Lectez, B., Migotti, R., Lee, S.Y., Ramirez, J., Beraza, N., Mansfield, B., Sutherland, J., Martinez-Chantar, M.L., Dittmar, G. and Mayor, U.
Journal of Proteome Research 13 (6): 3016-3026. 6 June 2014

Production of glycosylated soluble amyloid precursor protein alpha (sAPPalpha) in Leishmania tarentolae.
Klatt, S., Rohe, M., Alagesan, K., Kolarich, D., Konthur, Z. and Hartl, D.
Journal of Proteome Research 12 (1): 396-403. 4 January 2013

Presymptomatic alterations in energy metabolism and oxidative stress in the APP23 mouse model of Alzheimer disease.
Hartl, D., Schuldt, V., Forler, S., Zabel, C., Klose, J. and Rohe, M.
Journal of Proteome Research 11 (6): 3295-3304. 8 May 2012

Kainate promotes alterations in neuronal RNA splicing machinery.
Rohe, M., Nebrich, G., Klein, O., Mao, L., Zabel, C., Klose, J. and Hartl, D.
Journal of Proteome Research 10 (4): 1459-1467. 1 April 2011

Method for qualitative comparisons of protein mixtures based on enzyme-catalyzed stable-isotope incorporation.
Mirgorodskaya, E., Wanker, E.E., Otto, A., Lehrach, H. and Gobom, J.
Journal of Proteome Research 4 (6): 2109-2116. 1 November 2005