Publications

Cornelissen FMG, He Z, Ciputra E, de Haas RR, Beumer-Chuwonpad A, Noske D, Vandertop WP, Piersma SR, Jiménez CR, Murre C, Westerman BA. The translatome of glioblastoma. Mol Oncol. 2024 Oct 17. 

Podieh F, Overboom MC, Knol JC, Piersma SR, Goeij-de Haas R, Pham TV, Jimenez CR, Hordijk PL. AAMP and MTSS1 Are Novel Negative Regulators of Endothelial Barrier Function Identified in a Proteomics Screen. Cells. 2024 Sep 25;13(19):1609. 

Rombouts KB, van Merrienboer TAR, Henneman AA, Knol JC, Pham TV, Piersma SR, Jimenez CR, Bogunovic N, van der Velden J, Yeung KK. Insight in the (Phospho)proteome of Vascular Smooth Muscle Cells Derived From Patients With Abdominal Aortic Aneurysm Reveals Novel Disease Mechanisms. Arterioscler Thromb Vasc Biol. 2024 Oct;44(10):2226-2243. 

Lopez-Cerda M, Lorenzo-Sanz L, da Silva-Diz V, Llop S, Penin RM, Bermejo JO, de Goeij-de Haas R, Piersma SR, Pham TV, Jimenez CR, Martin-Liberal J, Muñoz P. IGF1R signaling induces epithelial-mesenchymal plasticity via ITGAV in cutaneous carcinoma. J Exp Clin Cancer Res. 2024 Jul 29;43(1):211. 

Pham TV, Henneman AA, Truong NX, Jimenez CR. msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease. Bioinformatics. 2024 Jul 1;40(7):btae432. 

Nollet EE, Schuldt M, Sequeira V, Binek A, Pham TV, Schoonvelde SAC, Jansen M, Schomakers BV, van Weeghel M, Vaz FM, Houtkooper RH, Van Eyk JE, Jimenez CR, Michels M, Bedi KC Jr, Margulies KB, Dos Remedios CG, Kuster DWD, van der Velden J. Integrating Clinical Phenotype With Multiomics Analyses of Human Cardiac Tissue Unveils Divergent Metabolic Remodeling in Genotype-Positive and Genotype-Negative Patients With Hypertrophic Cardiomyopathy. Circ Genom Precis Med. 2024 Jun;17(3):e004369. 

Suárez-Martínez E, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR, Carnero A. Protein homeostasis maintained by HOOK1 levels promotes the tumorigenic and stemness properties of ovarian cancer cells through reticulum stress and autophagy. J Exp Clin Cancer Res. 2024 May 29;43(1):150. 

Navarro-Carrasco E, Monte-Serrano E, Campos-Díaz A, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, González-Alonso P, Jiménez CR, Lazo PA. VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells. Int J Mol Sci. 2024 Apr 30;25(9):4874. 

Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol. 2024 Apr 22. 

Navarro-Carrasco E, Campos-Díaz A, Monte-Serrano E, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, Jiménez CR, Lazo PA. Loss of VRK1 alters the nuclear phosphoproteome in the DNA damage response to doxorubicin. Chem Biol Interact. 2024 Mar 1;391:110908. 

Rozemeijer S, Hamer HM, Heijboer AC, de Jonge R, Jimenez CR, Juffermans NP, Dujardin RWG, Girbes ARJ, de Man AME. Micronutrient Status of Critically Ill Patients with COVID-19 Pneumonia. Nutrients. 2024 Jan 29;16(3):385. 

Gali A, Bijnsdorp IV, Piersma SR, Pham TV, Gutiérrez-Galindo E, Kühnel F, Tsolakos N, Jimenez CR, Hausser A, Alexopoulos LG. Protein kinase D drives the secretion of invasion mediators in triple-negative breast cancer cell lines. iScience. 2024 Jan 17;27(2):108958. 

Gillette MA, Jimenez CR, Carr SA. Clinical Proteomics: A Promise Becoming Reality. Mol Cell Proteomics. 2024 Jan 27;23(2):100688. 

Almeida-Marques C, Rolfs F, Piersma SR, Bijnsdorp IV, Pham TV, Knol JC, Jimenez CR. Secretome processing for proteomics: A methods comparison. Proteomics. 2024 Jan 14:e2300262. 

Böttger F, Radonic T, Bahce I, Monkhorst K, Piersma SR, Pham TV, Dingemans AC, Hillen LM, Santarpia M, Giovannetti E, Smit EF, Burgers SA, Jimenez CR. Identification of protein biomarkers for prediction of response to platinum-based treatment regimens in patients with non-small cell lung cancer. Mol Oncol. 2023 Nov 27. doi:10.1002/1878-0261.13555. Epub ahead of print. PMID: 38010703.

van der Wijngaart H, Beekhof R, Knol JC, Henneman AA, de Goeij-de Haas R, Piersma SR, Pham TV, Jimenez CR, Verheul HMW, Labots M. Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics. Clin Proteomics. 2023 Nov 8;20(1):49. 

Beekhof R, Bertotti A, Böttger F, Vurchio V, Cottino F, Zanella ER, Migliardi G, Viviani M, Grassi E, Lupo B, Henneman AA, Knol JC, Pham TV, de Goeij-de Haas R, Piersma SR, Labots M, Verheul HMW, Trusolino L, Jimenez CR. Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer. Sci Transl Med. 2023 Aug 16;15(709):eabm3687. 

Rolfs F, de Goeij-de Haas RR, Knol JC, Piersma SR, Jimenez CR. Phosphoproteomics After Guanidinium Thiocyanate Extraction of Tissue Biopsies. Methods Mol Biol. 2023;2718:285-302. 

Erozenci LA, Bijnsdorp IV, Piersma SR, Jimenez CR. A Robust and Clinically Applicable Sample Preparation Protocol for Urinary Extracellular Vesicle Isolation Suitable for Mass Spectrometry-Based Proteomics. Methods Mol Biol. 2023;2718:235-251. 

Xue Z, Zhu T, Zhang F, Zhang C, Xiang N, Qian L, Yi X, Sun Y, Liu W, Cai X, Wang L, Dai X, Yue L, Li L, Pham TV, Piersma SR, Xiao Q, Luo M, Lu C, Zhu J, Zhao Y, Wang G, Xiao J, Liu T, Liu Z, He Y, Wu Q, Gong T, Zhu J, Zheng Z, Ye J, Li Y, Jimenez CR, A J, Guo T. DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins. Patterns (N Y). 2023 Jul 5;4(7):100792. 

Algül S, Schuldt M, Manders E, Jansen V, Schlossarek S, de Goeij-de Haas R, Henneman AA, Piersma SR, Jimenez CR, Michels M, Carrier L, Helmes M, van der Velden J, Kuster DWD. EGFR/IGF1R Signaling Modulates Relaxation in Hypertrophic Cardiomyopathy. Circ Res. 2023 Jul 21. 

Paciotti S, Wojdała AL, Bellomo G, Toja A, Chipi E, Piersma SR, Pham TV, Gaetani L, Jimenez CR, Parnetti L, Chiasserini D. Potential diagnostic value of CSF metabolism-related proteins across the Alzheimer’s disease continuum. Alzheimers Res Ther. 2023 Jul 15;15(1):124. 

Meulendijks ER, Al-Shama RFM, Kawasaki M, Fabrizi B, Neefs J, Wesselink R, Ernault AC, Piersma S, Pham TV, Jimenez CR, Knol JC, van Boven WJP, Driessen AHG, de Vries TAC, van der Leeden B, Niessen HWM, de Boer OJ, Krul SPJ, de Groot JR. Atrial epicardial adipose tissue abundantly secretes myeloperoxidase and activates atrial fibroblasts in patients with atrial fibrillation. J Transl Med. 2023 Jun 6;21(1):366. 

Vallés-Martí A, Mantini G, Manoukian P, Waasdorp C, Sarasqueta AF, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Giovannetti E, Bijlsma MF, Jiménez CR.  Phosphoproteomics guides effective low-dose drug combinations against pancreatic ductal adenocarcinoma. Cell Rep. 2023 Jun 1;42(6):112581. 

Bhin J, Paes Dias M, Gogola E, Rolfs F, Piersma SR, de Bruijn R, de Ruiter JR, van den Broek B, Duarte AA, Sol W, van der Heijden I, Andronikou C, Kaiponen TS, Bakker L, Lieftink C, Morris B, Beijersbergen RL, van de Ven M, Jimenez CR, Wessels LFA, Rottenberg S, Jonkers J. Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors. Cell Rep. 2023 May 30;42(5):112538. 

Chatterjee M, Özdemir S, Kunadt M, Koel-Simmelink M, Boiten W, Piepkorn L, Pham TV, Chiasserini D, Piersma SR, Knol JC, Möbius W, Mollenhauer B, van der Flier WM, Jimenez CR, Teunissen CE, Jahn O, Schneider A. C1q is increased in cerebrospinal fluid-derived extracellular vesicles in Alzheimer’s disease: A multi-cohort proteomics and immuno-assay validation study. Alzheimers Dement. 2023 Apr 6. 

Pham TV, Nguyen VV, Vu D, Henneman AA, Richardson RA, Piersma SR, Jimenez CR. A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics. Proteomics. 2023 Mar 12:e2200041. 

van der Wijngaart H, Jagga S, Dekker H, de Goeij R, Piersma SR, Pham TV, Knol JC, Zonderhuis BM, Holland HJ, Jiménez CR, Verheul HMW, Vanapalli S, Labots M. Advancing wide implementation of precision oncology: A liquid nitrogen-free snap freezer preserves molecular profiles of biological samples. Cancer Med. 2023 Mar 14. 

Pai G, Roohollahi K, Rockx D, de Jong Y, Stoepker C, Pennings C, Rooimans M, Vriend L, Piersma S, Jimenez CR, De Menezes RX, Van Beusechem VW, Brakenhoff RH, Te Riele H, Wolthuis RMF, Dorsman JC. Genome-wide siRNA screens identify RBBP9 function as a potential target in Fanconi anaemia-deficient head-and-neck squamous cell carcinoma. Commun Biol. 2023 Jan 13;6(1):37. 

Böttger F, Vallés-Martí A, Cahn L, Jimenez CR. High-dose intravenous vitamin C, a promising multi-targeting agent in the treatment of cancer. J Exp Clin Cancer Res. 2021 Oct 30;40(1):343. 

Erozenci LA, Pham TV, Piersma SR, Dits NFJ, Jenster GW, van Royen ME, Moorselaar RJA, Jimenez CR, Bijnsdorp IV. Simple urine storage protocol for extracellular vesicle proteomics compatible with at-home self-sampling. Sci Rep. 2021 Oct 21;11(1):20760. 

Walraven M, Sabrkhany S, Knol JC, Dekker H, de Reus I, Piersma SR, Pham TV, Griffioen AW, Broxterman HJ, Oude Egbrink M, Verheul HMW, Jimenez CR. Effects of Cancer Presence and Therapy on the Platelet Proteome. Int J Mol Sci. 2021 Jul 30;22(15):8236. 

Erozenci LA, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR. Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. Sci Rep. 2021 Aug 2;11(1):15629. 

de Klaver W, Wisse PHA, van Wifferen F, Bosch LJW, Jimenez CR, van der Hulst RWM, Fijneman RJA, Kuipers EJ, Greuter MJE, Carvalho B, Spaander MCW, Dekker E, Coupé VMH, de Wit M, Meijer GA. Clinical Validation of a Multitarget Fecal Immunochemical Test for Colorectal Cancer Screening : A Diagnostic Test Accuracy Study. Ann Intern Med. 2021 Sep;174(9):1224-1231. 

De Groof TWM, Bergkamp ND, Heukers R, Giap T, Bebelman MP, Goeij-de Haas R, Piersma SR, Jimenez CR, Garcia KC, Ploegh HL, Siderius M, Smit MJ. Selective targeting of ligand-dependent and -independent signaling by GPCR conformation-specific anti-US28 intrabodies. Nat Commun. 2021 Jul 16;12(1):4357. 

Cucchi DGJ, Van Alphen C, Zweegman S, Van Kuijk B, Kwidama ZJ, Al Hinai A, Henneman AA, Knol JC, Piersma SR, Pham TV, Jimenez CR, Cloos J, Janssen JJWM. Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors. Hemasphere. 2021 Jun 12;5(7):e606. 

Erdbrügger U, Blijdorp CJ, Bijnsdorp IV, Borràs FE, Burger D, Bussolati B, Byrd JB, Clayton A, Dear JW, Falcón-Pérez JM, Grange C, Hill AF, Holthöfer H, Hoorn EJ, Jenster G, Jimenez CR, Junker K, Klein J, Knepper MA, Koritzinsky EH, Luther JM, Lenassi M, Leivo J, Mertens I, Musante L, Oeyen E, Puhka M, van Royen ME, Sánchez C, Soekmadji C, Thongboonkerd V, van Steijn V, Verhaegh G, Webber JP, Witwer K, Yuen PST, Zheng L, Llorente A, Martens-Uzunova ES. Urinary extracellular vesicles: A position paper by the Urine Task Force of the International Society for Extracellular Vesicles. J Extracell Vesicles. 2021 May;10(7):e12093. 

Li RE, de Haas A, Rodríguez E, Kalay H, Zaal A, Jimenez CR, Piersma SR, Pham TV, Henneman AA, de Goeij-de Haas RR, van Vliet SJ, van Kooyk Y. Quantitative Phosphoproteomic Analysis Reveals Dendritic Cell- Specific STAT Signaling After α2-3-Linked Sialic Acid Ligand Binding. Front Immunol. 2021 Apr 22;12:673454. 

Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep. 2021 Jun 4;22(6):e51913. 

Rolfs F, Piersma SR, Dias MP, Jonkers J, Jimenez CR. Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate. Mol Cell Proteomics. 2021 Apr 2;20:100078. 

Le Large TYS, Bijlsma MF, El Hassouni B, Mantini G, Lagerweij T, Henneman AA, Funel N, Kok B, Pham TV, de Haas R, Morelli L, Knol JC, Piersma SR, Kazemier G, van Laarhoven HWM, Giovannetti E, Jimenez CR. Focal adhesion kinase inhibition synergizes with nab-paclitaxel to target pancreatic ductal adenocarcinoma. J Exp Clin Cancer Res. 2021 Mar 9;40(1):91. 

Schuldt M, Dorsch LM, Knol JC, Pham TV, Schelfhorst T, Piersma SR, Dos Remedios C, Michels M, Jimenez CR, Kuster DWD, van der Velden J. Sex-Related Differences in Protein Expression in Sarcomere Mutation-Positive Hypertrophic Cardiomyopathy. Front Cardiovasc Med. 2021 Mar 1;8:612215. 

Buffart TE, van den Oord RAHM, van den Berg A, Hilhorst R, Bastiaensen N, Pruijt HFM, van den Brule A, Nooijen P, Labots M, de Goeij-de Haas RR, Dekker H, Piersma SR, Pham TV, van der Leij T, de Wijn R, Ruijtenbeek R, Jiménez CR, Verheul HMW. Time dependent effect of cold ischemia on the phosphoproteome and protein kinase activity in fresh-frozen colorectal cancer tissue obtained from patients. Clin Proteomics. 2021 Feb 18;18(1):8.,

de Durango CRG, Monteiro MN, Bijnsdorp IV, Pham TV, De Wit M, Piersma SR, Knol JC, Pérez-Gordo M, Fijneman RJA, Vidal-Vanaclocha F, Jimenez CR. Lipopolysaccharide-regulated secretion of soluble and vesicle-based proteins from a panel of colorectal cancer cell lines. Proteomics Clin Appl. 2021 Feb 15:e1900119.

van Alphen C, Cucchi DGJ, Cloos J, Schelfhorst T, Henneman AA, Piersma SR, Pham TV, Knol JC, Jimenez CR, Janssen JJWM. The influence of delay in mononuclear cell isolation on acute myeloid leukemia phosphorylation profiles. J Proteomics. 2021 Feb 6:104134.

Kawasaki M, Meulendijks ER, van den Berg NWE, Nariswari FA, Neefs J, Wesselink R, Baalman SWE, Jongejan A, Schelfhorst T, Piersma SR, Pham TV, van Boven WJP, Driessen AHG, Jimenez CR, de Groot JR. Neutrophil degranulation interconnects over-represented biological processes in atrial fibrillation. Sci Rep. 2021 Feb 3;11(1):2972.

Glykofrid IE, Knol JC, Balk JA, Westland D, Pham TV, Piersma SR, Lougheed SM, Derakhshan S, Veen P, Rooimans MA, van Mil SE, Böttger F, Poddighe PJ, van de Beek I, Drost J, Zwartkruis FJT, de Menezes RX, Meijers-Heijboer HEJ, Houweling AC, Jimenez CR, Wolthuis RMF.  Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells. eLife 2021. https://elifesciences.org/articles/61630

den Uil SH, de Wit M, Slebos RJC, Delis-van Diemen PM, Sanders J, Piersma SR, Pham TV, Coupé VMH, Bril H, Stockmann HBAC, Jimenez CR, Meijer GA, Fijneman RJA. Quantitative analysis of CDX2 protein expression improves its clinical utility as a prognostic biomarker in stage II and III colon cancer. Eur J Cancer. 144:91-100. doi: 10.1016/j.ejca.2020.10.029. Epub ahead of print. PMID: 33341450.

Schuldt M, Pei J, Harakalova M, Dorsch LM, Schlossarek S, Mokry M, Knol JC, Pham TV, Schelfhorst T, Piersma SR, Dos Remedios C, Dalinghaus M, Michels M, Asselbergs FW, Moutin MJ, Carrier L, Jimenez CR, van der Velden J, Kuster DWD. Proteomic and Functional Studies Reveal Detyrosinated Tubulin as Treatment Target in Sarcomere Mutation-Induced Hypertrophic Cardiomyopathy. Circ Heart Fail. 2021 Jan 12:CIRCHEARTFAILURE120007022. doi: 10.1161/CIRCHEARTFAILURE.120.007022. Epub ahead of print. PMID: 33430602.

Mantini G, Meijer LL, Glogovitis I, In ‘t Veld SGJG, Paleckyte R, Capula M, Le Large TYS, Morelli L, Pham TV, Piersma SR, Frampton AE, Jimenez CR, Kazemier G, Koppers-Lalic D, Wurdinger T, Giovannetti E. Omics Analysis of Educated Platelets in Cancer and Benign Disease of the Pancreas. Cancers 2021, 13(1), 66; https://doi.org/10.3390/cancers13010066.

2020

Yue Xuan, Nicholas W. Bateman, Sebastien Gallien, Sandra Goetze, Yue Zhou, Pedro Navarro, Mo Hu, Niyati Parikh, Brian L. Hood, Kelly A. Conrads, Christina Loosse, Reta Birhanu Kitata, Sander R. Piersma, Davide Chiasserini, Hongwen Zhu, Guixue Hou, Muhammad Tahir, Andrew Macklin, Amanda Khoo, Xiuxuan Sun, Ben Crossett, Albert Sickmann, Yu-Ju Chen, Connie R. Jimenez, Hu Zhou, Siqi Liu, Martin R. Larsen, Thomas Kislinger, Zhinan Chen, Benjamin L. Parker, Stuart J. Cordwell, Bernd Wollscheid, Thomas P. Conrads. Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies. Nature Communications 11(1):5248; doi: 10.1038/s41467-020-18904-9.

Mantini G, Pham TV, Piersma SR, Jimenez CR. Computational Analysis of Phosphoproteomics Data in Multi-Omics Cancer Studies. Proteomics. 2020 Sep 1:e1900312.

Mantini G, Vallés AM, Le Large TYS, Capula M, Funel N, Pham TV, Piersma SR, Kazemier G, Bijlsma MF, Giovannetti E, Jimenez CR. Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers. Cell Oncol (Dordr). 2020 Aug 29. doi: 10.1007/s13402-020-00548-y. Epub ahead of print. PMID: 32860207.

van den Berg I, van de Weerd S, Roodhart JML, et al. Improving clinical management of colon cancer through CONNECTION, a nation-wide colon cancer registry and stratification effort (CONNECTION II trial): rationale and protocol of a single arm intervention study. BMC Cancer. 2020;20(1):776. Published 2020 Aug 18. doi:10.1186/s12885-020-07236-y

Zhu T, Zhu Y, Xuan Y, Gao H, Cai X, Piersma SR, Pham TV, Schelfhorst T, Haas RRGD, Bijnsdorp IV, Sun R, Yue L, Ruan G, Zhang Q, Hu M, Zhou Y, Van Houdt WJ, Lelarge TYS, Cloos J, Wojtuszkiewicz A, Koppers-Lalic D, Böttger F, Scheepbouwer C, Brakenhoff RH, van Leenders GJLH, Ijzermans JNM, Martens JWM, Steenbergen RDM, Grieken NC, Selvarajan S, Mantoo S, Lee SS, Yeow SJY, Alkaff SMF, Xiang N, Sun Y, Yi X, Dai S, Liu W, Lu T, Wu Z, Liang X, Wang M, Shao Y, Zheng X, Xu K, Yang Q, Meng Y, Lu C, Zhu J, Zheng J, Wang B, Lou S, Dai Y, Xu C, Yu C, Ying H, Lim TK, Wu J, Gao X, Luan Z, Teng X, Wu P, Huang S, Tao Z, Iyer NG, Zhou S, Shao W, Lam H, Ma D, Ji J, Kon OL, Zheng S, Aebersold R, Jimenez CR, Guo T. DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genomics Proteomics Bioinformatics. 2020 Aug 11:S1672-0229(20)30093-0.

Le Large TY, Mantini G, Meijer LL, Pham TV, Funel N, van Grieken NC, Kok B, Knol J, van Laarhoven HW, Piersma SR, Jimenez CR, Kazemier G, Giovannetti E, Bijlsma MF. Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets. JCI Insight. 2020 Aug 6;5(15):138290.

van Steenoven I, Koel-Simmelink MJA, Vergouw LJM, Tijms BM, Piersma SR, Pham TV, Bridel C, Ferri GL, Cocco C, Noli B, Worley PF, Xiao MF, Xu D, Oeckl P, Otto M, van der Flier WM, de Jong FJ, Jimenez CR, Lemstra AW, Teunissen CE. Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach. Mol Neurodegener. 2020 Jun 18;15(1):36.

González-Alonso P, Zazo S, Martín-Aparicio E, Luque M, Chamizo C, Sanz-Álvarez M, Minguez P, Gómez-López G, Cristóbal I, Caramés C, García-Foncillas J, Eroles P, Lluch A, Arpí O, Rovira A, Albanell J, Piersma SR, Jimenez CR, Madoz-Gúrpide J, Rojo F. The Hippo Pathway Transducers YAP1/TEAD Induce Acquired Resistance to Trastuzumab in HER2-Positive Breast Cancer. Cancers (Basel). 2020 Apr 29;12(5):1108.

van Alphen C, Cloos J, Beekhof R, Cucchi DGJ, Piersma SR, Knol JC, Henneman AA, Pham TV, van Meerloo J, Ossenkoppele GJ, Verheul HM, Janssen JJ, Jimenez CR. Phosphotyrosine-based phosphoproteomics for target identification and drug response prediction in AML cell lines. Mol Cell Proteomics. 2020 Feb 26. pii: mcp.RA119.001504.

Labots M, Pham TV, Honeywell RJ, Knol JC, Beekhof R, de Goeij-de Haas R, Dekker H, Neerincx M, Piersma SR, van der Mijn JC, van der Peet DL, Meijerink MR, Peters GJ, van Grieken NCT, Jiménez CR, Verheul HMW. Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome. Cancers (Basel). 2020 Feb 1;12(2). pii: E330. doi: 10.3390/cancers12020330. PubMed PMID: 32024067.

Turaihi AH, Serné EH, Molthoff CF, Koning JJ, Knol J, Niessen HW, Jose Th Goumans M, van Poelgeest EM, Yudkin JS, Smulders YM, Jimenez CR, van Hinsbergh VW, Eringa EC. Perivascular Adipose Tissue Controls Insulin-Stimulated Perfusion, Mitochondrial Protein Expression and Glucose Uptake in Muscle Through Adipomuscular Arterioles. Diabetes. 2020 Jan 31. pii: db181066. doi: 10.2337/db18-1066.

Le Large TYS, Meijer LL, Paleckyte R, Boyd LNC, Kok B, Wurdinger T, Schelfhorst T, Piersma SR, Pham TV, van Grieken NCT, Zonderhuis BM, Daams F, van Laarhoven HWM, Bijlsma MF, Jimenez CR, Giovannetti E, Kazemier G. Combined Expression of Plasma Thrombospondin-2 and CA19-9 for Diagnosis of Pancreatic Cancer and Distal Cholangiocarcinoma: A Proteome Approach. Oncologist. 2020 Jan 14.

Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics. 2020 Jan 7. pii: btz961.

Komor MA, Bosch LJ, Coupé VM, Rausch C, Pham TV, Piersma SR, Mongera S, Mulder CJ, Dekker E, Kuipers EJ, van de Wiel MA, Carvalho B, Fijneman RJ, Jimenez CR, Meijer GA, de Wit M. Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression. J Pathol. 2020 Mar;250(3):288-298.

2019

López González M, Oosterhoff D, Lindenberg JJ, Milenova I, Lougheed SM, Martiáñez T, Dekker H, Quixabeira DCA, Hangalapura B, Joore J, Piersma SR, Cervera-Carrascon V, Santos JM, Scheper RJ, Verheul HMW, Jiménez CR, Van De Ven R, Hemminki A, Van Beusechem VW, De Gruijl TD. Constitutively active GSK3β as a means to bolster dendritic cell functionality in the face of tumour-mediated immune suppression. Oncoimmunology. 2019 Jul 19;8(10):e1631119.

Poel D, Boyd LNC, Beekhof R, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Jimenez CR, Verheul HMW, Buffart TE. Proteomic Analysis of miR-195 and miR-497 Replacement Reveals Potential Candidates that Increase Sensitivity to Oxaliplatin in MSI/P53wt Colorectal Cancer Cells. Cells. 2019 Sep 19;8(9). pii: E1111.

El Hassouni B, Granchi C, Vallés-Martí A, Supadmanaba IGP, Bononi G, Tuccinardi T, Funel N, Jimenez CR, Peters GJ, Giovannetti E, Minutolo F. The dichotomous role of the glycolytic metabolism pathway in cancer metastasis: Interplay with the complex tumor microenvironment and novel therapeutic strategies. Semin Cancer Biol. 2019 Aug 21. pii: S1044-579X(19)30180-4. 

Komor MA, de Wit M, van den Berg J, Martens de Kemp SR, Delis-van Diemen PM, Bolijn AS, Tijssen M, Schelfhorst T, Piersma SR, Chiasserini D, Sanders J, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, Carvalho B, Meijer GA, Jimenez CR, Fijneman RJA; NGS-ProToCol Consortium. Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression. Int J Cancer. 2019 Aug 14.

Le Large TYS, El Hassouni B, Funel N, Kok B, Piersma SR, Pham TV, Olive KP, Kazemier G, van Laarhoven HWM, Jimenez CR, Bijlsma MF, Giovannetti E. Proteomic analysis of gemcitabine-resistant pancreatic cancer cells reveals that microtubule-associated protein 2 upregulation associates with taxane treatment. Ther Adv Med Oncol. 2019 May 10;11:1758835919841233.

Erozenci LA, Böttger F, Bijnsdorp IV, Jimenez CR. Urinary exosomal proteins as (pan-)cancer biomarkers: insights from the proteome. FEBS Lett. 2019 Jul;593(13):1580-1597.

Böttger F, Semenova EA, Song JY, Ferone G, van der Vliet J, Cozijnsen M, Bhaskaran R, Bombardelli L, Piersma SR, Pham TV, Jimenez CR, Berns A. Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer. Cell Rep. 2019 Jun 11;27(11):3345-3358.e4.

Beekhof R, van Alphen C, Henneman AA, Knol JC, Pham TV, Rolfs F, Labots M, Henneberry E, Le Large TY, de Haas RR, Piersma SR, Vurchio V, Bertotti A, Trusolino L, Verheul HM, Jimenez CR. INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases. Mol Syst Biol. 2019 Apr 12;15(4):e8250. doi: 10.15252/msb.20188250. PubMed PMID: 30979792; PubMed Central PMCID: PMC6461034.

Rolfs F, Piersma SR, Jimenez CR. Re-assessment of the high-grade serous ovarian cancer phosphoproteome – Identification of kinase candidates in TCGA tumors for future clinical intervention. EBioMedicine. 2019 Mar;41:34-35. doi: 10.1016/j.ebiom.2019.02.018. Epub 2019 Feb 21. PubMed PMID: 30797713; PubMed Central PMCID: PMC6442312.

Böttger F, Schaaij-Visser TB, de Reus I, Piersma SR, Pham TV, Nagel R, Brakenhoff RH, Thunnissen E, Smit EF, Jimenez CR. Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction. J Proteomics. 2019 Mar 30;196:106-119. doi: 10.1016/j.jprot.2019.01.018. Epub 2019 Jan 30. PubMed PMID: 30710758.

Castillo J, Knol JC, Korver CM, Piersma SR, Pham TV, de Goeij-de Haas RR, van Pelt AMM, Jimenez CR, Jansen BJH. Human Testis Phosphoproteome Reveals Kinases as Potential Targets in Spermatogenesis and Testicular Cancer. Mol Cell Proteomics. 2019 Mar 15;18(Suppl 1):S132-S144. doi: 10.1074/mcp.RA118.001278. Epub 2019 Jan 25. PubMed PMID: 30683686; PubMed Central PMCID: PMC6427237.

2018

Le Large TYS, El Hassouni B, Kazemier G, Piersma SR, van Laarhoven HWM, Bijlsma MF, Jimenez CR, Giovannetti E. Multidrug-resistant transporter expression does not always result in drug resistance. Cancer Sci. 2018 Oct;109(10):3360-3362.

Phan TH, van Leeuwen LM, Kuijl C, Ummels R, van Stempvoort G, Rubio-Canalejas A, Piersma SR, Jiménez CR, van der Sar AM, Houben ENG, Bitter W. EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF. PLoS Pathog. 2018 Aug 13;14(8):e1007247.

Stokman MF, Bijnsdorp IV, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Giles RH, Bongers EMHF, Knoers NVAM, Lilien MR, Jiménez CR, Renkema KY. Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies. J Proteomics. 2018 Jul 30. pii:S1874-3919(18)30278-1.

Komor MA, Bosch LJ, Bounova G, Bolijn AS, van-Diemen PD, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, van Grieken NC, Carvalho B, Wessels LF, Jimenez CR, Fijneman RJ, Meijer GA; NGS-ProToCol Consortium, Dits N, Böttcher R, Hiemstra AC, Ylstra B, Sie D, van den Broek E, van der Meer D, Pepers F, Caldenhoven E, Janssen B, van Workum W, van Lieshout S, Bangma CH, van Leenders G, van de Werken H.
Consensus molecular subtypes classification of colorectal adenomas. J Pathol. 2018 Jul 3. doi: 10.1002/path.5129.

Steenbeek SC, Pham TV, de Ligt J, Zomer A, Knol JC, Piersma SR, Schelfhorst T, Huisjes R, Schiffelers RM, Cuppen E, Jimenez CR*, van Rheenen J*. Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles. EMBO J. 2018 Jun 14. pii: e8357. doi: 10.15252/embj.201798357. [Epub ahead of print]
PMID: 29907695 Shared senior authors.

Bijnsdorp IV, Jimenez CR. Large-Scale Urinary Proteome Dataset Across Tumor Types Reveals Candidate Biomarkers for Lung Cancer. EBioMedicine. 2018 Mar 14.  pii: S2352-3964(18)30096-3.

Sabrkhany S, Kuijpers MJE, Knol JC, Olde Damink SWM, Dingemans AC, Verheul HM,  Piersma SR, Pham TV, Griffioen AW, Oude Egbrink MGA, Jimenez CR. Exploration of the platelet proteome in patients with early-stage cancer. J Proteomics. 2018 Apr 15;177:65-74.

Jimenez CR, Zhang H, Kinsinger CR, Nice EC. The cancer proteomic landscape and the HUPO Cancer Proteome Project. Clin Proteomics. 2018 Jan 25;15:4.

Verweij FJ, Bebelman MP, Jimenez CR, Garcia-Vallejo JJ, Janssen H, Neefjes J,  Knol JC, de Goeij-de Haas R, Piersma SR, Baglio SR, Verhage M, Middeldorp JM,  Zomer A, van Rheenen J, Coppolino MG, Hurbain I, Raposo G, Smit MJ, Toonen RFG,  van Niel G, Pegtel DM. Quantifying exosome secretion from single cells reveals a  modulatory role for GPCR signaling. J Cell Biol. 2018 Mar 5;217(3):1129-1142.

Ates LS, Dippenaar A, Ummels R, Piersma SR, van der Woude AD, van der Kuij K,  Le Chevalier F, Mata-Espinosa D, Barrios-Payán J, Marquina-Castillo B, Guapillo C, Jiménez CR, Pain A, Houben ENG, Warren RM, Brosch R, Hernández-Pando R, Bitter W. Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis. Nat Microbiol. 2018 Feb;3(2):181-188.

Bijen HM, Hassan C, Kester MGD, Janssen GMC, Hombrink P, de Ru AH, Drijfhout JW, Meiring HD, de Jong AP, Falkenburg JHF, Jimenez CR, Heemskerk MHM, van Veelen PA. Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface. Proteomics. 2018 Jun;18(12):e1700250. doi: 10.1002/pmic.201700250. Epub 2018 Feb 23.

Bridel C, Koel-Simmelink MJA, Peferoen L, Derada Troletti C, Durieux S, Gorter R, Nutma E, Gami P, Iacobaeus E, Brundin L, Kuhle J, Vrenken H, Killestein J, Piersma SR, Pham TV, De Vries HE, Amor S, Jimenez CR, Teunissen CE. Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro. Neuropathol Appl Neurobiol. 2018 Jun;44(4):404-416. doi: 10.1111/nan.12412. Epub 2017 Jun 28.

2017

• Bosch LJW, de Wit M, Pham TV, Coupé VMH, Hiemstra AC, Piersma SR, Oudgenoeg G, Scheffer GL, Mongera S, Sive Droste JT, Oort FA, van Turenhout ST, Larbi IB, Louwagie J, van Criekinge W, van der Hulst RWM, Mulder CJJ, Carvalho B, Fijneman RJA, Jimenez CR, Meijer GA. Novel Stool-Based Protein Biomarkers for Improved Colorectal Cancer Screening: A Case-Control Study. Ann Intern Med. 2017 Dec 19;167(12):855-866.
• Van der Hiel B, Haanen JBAG, Stokkel MPM, Peeper DS, Jimenez CR, Beijnen JH, van de Wiel BA, Boellaard R, van den Eertwegh AJM; REPOSIT study group. Vemurafenib plus cobimetinib in unresectable stage IIIc or stage IV melanoma: response monitoring and resistance prediction with positron emission tomography and tumor characteristics (REPOSIT): study protocol of a phase II, open-label, multicenter study. BMC Cancer. 2017 Sep 15;17(1):649.
• Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA. Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. Mol Cell Proteomics. 2017 Oct;16(10):1850-1863.
• Bijnsdorp IV, Maxouri O, Kardar A, Schelfhorst T, Piersma SR, Pham TV, Vis A, van Moorselaar RJ, Jimenez CR. Feasibility of urinary extracellular vesicle proteome profiling using a robust and simple, clinically applicable isolation method. J Extracell Vesicles. 2017 Apr 28;6(1):1313091.
• Bridel C, Koel-Simmelink MJA, Peferoen L, Derada Troletti C, Durieux S, Gorter R, Nutma E, Gami P, Iacobaeus E, Brundin L, Kuhle J, Vrenken H, Killestein J, Piersma SR, Pham TV, De Vries HE, Amor S, Jimenez CR, Teunissen CE. Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro. Neuropathol ApplNeurobiol. 2017 May 24. doi: 10.1111/nan.12412. [Epub ahead of print] PubMedPMID: 28543098.
• Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NCT, Verheul HMW, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics. 2017 Jun6;162:99-107.
• Le Large TYS, Bijlsma MF, Kazemier G, van Laarhoven HWM, Giovannetti E, Jimenez CR. Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies. Semin Cancer Biol. 2017Jun;44:153-169.

2016

• Labots M, Gotink KJ, Dekker H, Azijli K, van der Mijn JC, Huijts CM, Piersma SR, Jiménez CR, Verheul HM. Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer. Exp Mol Med. 2016 Dec 16;48(12):e279.
• Van Winden VJ, Ummels R, Piersma SR, Jiménez CR, Korotkov KV, Bitter W, Houben EN. Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes. MBio. 2016 Oct 18;7(5). pii: e01471-16.
• Pham TV, Jimenez CR. Simulated linear test applied to quantitative proteomics. Bioinformatics. 2016 Sep 1;32(17):i702-i709. doi: 10.1093/bioinformatics/btw440. PubMed PMID: 27587692.
• Warmoes M, Lam SW, der Groep PV, Jaspers JE, Smolders YH, de Boer L, Pham TV, Piersma SR, Rottenberg S, Boven E, Jonkers J, van Diest PJ, Jimenez CR. Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget. 2016 Aug 23. doi: 10.18632/oncotarget.11535. [Epub ahead of print] PubMed PMID: 27566577.
• Schouten M, Bielefeld P, Fratantoni SA, Hubens CJ, Piersma SR, Pham TV, Voskuyl RA, Lucassen PJ, Jimenez CR, Fitzsimons CP. Multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus. Sci Data. 2016 Aug 16;3:160068.
• van Linde ME, van der Mijn JC, Pham TV, Knol JC, Wedekind LE, Hovinga KE, Aliaga ES, Buter J, Jimenez CR, Reijneveld JC, Verheul HM. Evaluation of potential circulating biomarkers for prediction of response to chemoradiation in patients with glioblastoma. J Neurooncol. 2016 Sep;129(2):221-30.
• Teunissen CE, Elias N, Koel-Simmelink MJ, Durieux-Lu S, Malekzadeh A, Pham TV, Piersma SR, Beccari T, Meeter LH, Dopper EG, van Swieten JC, Jimenez CR, Pijnenburg YA. Novel diagnostic cerebrospinal fluid biomarkers for pathologic subtypes of frontotemporal dementia identified by proteomics. Alzheimers Dement (Amst). 2016 Jan 19;2:86-94.
• Rovithi M, Lind JS, Pham TV, Voortman J, Knol JC, Verheul HM, Smit EF, Jimenez CR. Response and toxicity prediction by MALDI-TOF-MS serum peptide profiling in patients with non-small cell lung cancer. Proteomics Clin Appl. 2016 Jul;10(7):743-9.
• van der Mijn JC, Broxterman HJ, Knol JC, Piersma SR, De Haas RR, Dekker H, Pham TV, Van Beusechem VW, Halmos B, Mier JW, Jiménez CR, Verheul HM. Sunitinib activates Axl signaling in renal cell cancer. Int J Cancer. 2016 Jun 15;138(12):3002-10.
• Jaco C. Knol, Inge de Reus, Tim Schelfhorst, Robin Beekhof, Meike de Wit, Sander R. Piersma, Thang V. Pham, Egbert F. Smit, Henk M.W. Verheul, Connie R. Jiménez. Peptide-mediated ‘miniprep’ isolation of extracellular vesicles is suitable for high-throughput proteomics. EuPA Open Proteomics Volume 11, June 2016, Pages 11–15. http://dx.doi.org/10.1016/j.euprot.2016.02.001
• Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR. Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis. Mol Cell Proteomics. 2016 Apr;15(4):1281-98.
• Baglio SR, van Eijndhoven MA, Koppers-Lalic D, Berenguer J, Lougheed SM, Gibbs S, Léveillé N, Rinkel RN, Hopmans ES, Swaminathan S, Verkuijlen SA, Scheffer GL, van Kuppeveld FJ, de Gruijl TD, Bultink IE, Jordanova ES, Hackenberg M, Piersma SR, Knol JC, Voskuyl AE, Wurdinger T, Jiménez CR, Middeldorp JM, Pegtel DM. Sensing of latent EBV infection through exosomal transfer of 5’pppRNA. Proc Natl Acad Sci USA. 2016 Feb 2;113(5):E587-96.
• Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ. Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling. Am J Physiol Renal Physiol. 2015 Nov 11:ajprenal.00429.2015.

2015

Schouten M, Fratantoni SA, Hubens CJ, Piersma SR, Pham TV, Bielefeld P, Voskuyl RA, Lucassen PJ, Jimenez CR, Fitzsimons CP. MicroRNA-124 and -137 cooperativity controls caspase-3 activity through BCL2L13 in hippocampal neural stem cells.Sci Rep. 2015 Jul 24;5:12448.

Ates LS, Ummels R, Commandeur S, van de Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria.PLoS Genet. 2015 May 4;11(5):e1005190.

van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR. Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomicsJ Proteomics. 2015 Sep 8;127(Pt B):259-63.

Verweij FJ, de Heus C, Kroeze S, Cai H, Kieff E, Piersma SR, Jimenez CR, Middeldorp JM, Pegtel DM. Exosomal sorting of the viral oncoprotein LMP1 is restrained by TRAF2 association at signalling endosomes.J Extracell Vesicles. 2015 Apr 10;4:26334

Grinberg LT, Jimenez CR, Li KW. Neuroproteomics: applications in neuroscience and neurology.Biochim Biophys Acta. 2015 Jul;1854(7):703-4.

Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR. Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines.J Proteomics. 2015 Sep 8;127(Pt B):247-58.

Nagel R, Stigter-van Walsum M, Buijze M, van den Berg J, van der Meulen IH, Hodzic J, Piersma SR, Pham TV, Jimenez CR, van Beusechem VW, Brakenhoff RH. Genome-wide siRNA screen identifies the radiosensitizing effect of downregulation of MASTL and FOXM1 in NSCLC. Mol Cancer Ther. 2015 Mar 25. pii: molcanther.0846.2014. [Epub ahead of print] PubMed PMID: 25808837.

Del Campo Milan M, Zuroff L, Jimenez CR, Scheltens P, Teunissen CE. Can agrin cerebrospinal fluid concentration be used as an early biomarker for Alzheimer’s disease? Alzheimers Dement (Amst). 2015 Mar 29;1(1):75-80. doi: 10.1016/j.dadm.2014.11.008. eCollection 2015 Mar.

Jimenez CR, Fijneman RJ. Proteomics of Colorectal Cancer in a Genomic Context: First Large-Scale Mass Spectrometry-Based Analysis from the Cancer Genome Atlas. Clin Chem. 2015 Feb 26. pii: clinchem.2014.234807. [Epub ahead of print] PubMed PMID: 25722459.

2014

• Van der Mijn JC, Sol N, Mellema W, Jimenez CR, Piersma SR, Dekker H, Schutte LM, Smit EF, Broxterman HJ, Skog J, Tannous BA, Wurdinger T, Verheul HM. Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer. J Extracell Vesicles. 2014 Dec 8;3:25657. doi: 10.3402/jev.v3.25657. eCollection 2014. PubMed PMID: 25491250; PubMed Central PMCID: PMC4261239.
• Emmink BL, Laoukili J, Kipp AP, Koster J, Govaert KM, Fatrai S, Verheem A, Steller EJ, Brigelius-Flohe R, Jimenez CR, Borel Rinkes IH, Kranenburg O. GPx2 suppression of H2O2 stress links the formation of differentiated tumor mass to metastatic capacity in colorectal cancer. Cancer Res. 2014 Sep 26. pii: canres.1645.2014. [Epub ahead of print]
• Labots M, Schütte LM, van der Mijn JC, Pham TV, Jiménez CR, Verheul HM. Mass Spectrometry-Based Serum and Plasma Peptidome Profiling for Prediction of Treatment Outcome in Patients With Solid Malignancies. Oncologist. 2014 Oct;19(10):1028-1039. Epub 2014 Sep 3. Review.
• Rajcevic U, Knol JC, Piersma S, Bougnaud S, Fack F, Sundlisaeter E, Søndenaa K, Myklebust R, Pham TV, Niclou SP, Jiménez CR. Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture. Proteome Sci. 2014 Jul 11;12:39.
• Hassan C, Kester MG, Oudgenoeg G, de Ru AH, Janssen GM, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MH, Falkenburg JH, van Veelen PA. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J. Proteomics 2014 Jul 19;109C:240-244.
• Daleke-Schermerhorn MH, Felix T, Soprova Z, Ten Hagen-Jongman CM, Vikström D, Majlessi L, Beskers J, Follmann F, de Punder K, van der Wel NN, Baumgarten T, Pham TV, Piersma SR, Jiménez CR, van Ulsen P, de Gier JW, Leclerc C, Jong WS, Luirink J. Decoration of outer membrane vesicles with multiple antigens by using an autotransporter approach. Appl Environ Microbiol. 2014 Sep;80(18):5854-65.
• Senol O, Schaaij-Visser TB, Erkan EP, Dorfer C, Lewandrowski G, Pham TV, Piersma SR, Peerdeman SM, Ströbel T, Tannous B, Saydam N, Slavc I, Knosp E, Jimenez CR, Saydam O. miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo. Oncogene. 2014 May 26;0.
• Jimenez CR, Verheul HM. Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications. Am Soc Clin Oncol Educ Book. 2014;34:e504-10. doi: 10.14694/EdBook_AM.2014.34.e504. PubMed PMID: 24857147.
• Chiasserini D, van Weering JR, Piersma SR, Pham TV, Malekzadeh A, Teunissen CE, de Wit H, Jiménez CR. Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset. J Proteomics. 2014 Apr 24;106C:191-204.
• Del Campo M, Hoozemans JJ, Dekkers LL, Rozemuller AJ, Korth C, Müller-Schiffmann A, Scheltens P, Blankenstein MA, Jimenez CR, Veerhuis R, Teunissen CE. BRI2-BRICHOS is increased in human amyloid plaques in early stages of Alzheimer’s disease. Neurobiol Aging. 2014 Jul;35(7):1596-604.
• De Wit M, Kant H, Piersma SR, Pham TV, Mongera S, van Berkel MP, Boven E, Pontén F, Meijer GA, Jimenez CR*, Fijneman RJ*. Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling. J Proteomics. 2014 Jan 10; 99C: 269-39. *Shared senior authorship.
• Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: Current state of knowledge. Cancer Treat Rev. 2014 Feb; 40(1): 129-38.

2013

• Knol JC, de Wit M, Albrethsen J, Piersma SR, Pham TV, Mongera S, Carvalho B, Fijneman RJA, Meijer GA, Jiménez CR. Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues. Biochim Biophys Acta – Proteins and Proteomics (2013).
• Bijnsdorp IV, Geldof AA, Lavaei M, Piersma SR, van Moorselaar RJA, Jimenez CR. ITGA3 and ITGB1 interfere with non-cancerous prostate cell functions and are increased in urine exosomes of metastatic prostate cancer patients. J Extracell Vesicles. 2013 Dec 23;2.
• Van der Woude AD, Stoop EJ, Stiess M, Wang S, Ummels R, van Stempvoort G, Piersma SR, Cascioferro A, Jiménez CR, Houben EN, Luirink J, Pieters J, van der Sar AM, Bitter W. Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector. Cell Microbiol. 2013 Oct 9.
• Kooij V, Zhang P, Piersma SR, Sequeira V, Boontje NM, Wijnker PJ, Jiménez CR, Jaquet KE, Dos Remedios C, Murphy AM, Van Eyk JE, van der Velden J, Stienen GJ. PKCα-Specific Phosphorylation of the Troponin Complex in Human Myocardium: A Functional and Proteomics Analysis. PLoS One. 2013 Oct 7;8(10): e74847.
• Posthumadeboer J, Piersma SR, Pham TV, van Egmond PW, Knol JC, Cleton-Jansen AM, van Geer MA, van Beusechem VW, Kaspers GJ, van Royen BJ, Jiménez CR, Helder MN. Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery. Br J Cancer. 2013 Oct 15;109(8):2142-54. doi: 10.1038/bjc.2013.578. Epub 2013 Sep 24.
• Snoeren N, Emmink BL, Koerkamp MJ, van Hooff SR, Goos JA, van Houdt WJ, de Wit M, Prins AM, Piersma SR, Pham TV, Belt EJ, Bril H, Stockmann HB, Meijer GA, van Hillegersberg R, Holstege FC, Jimenez CR, Fijneman RJ, Kranenburg OW, Rinkes IH. Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer. PLoS One. 2013 Sep 17;109(6): 1636-47.
• DeBoer JP, Piersma SR, Pham TV, Knol JC, van Beusechem VW, Kaspers GJL, van Royen BJ, Jiménez CR, Helder MN*. Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery. British Journal of Cancer (2013). *Shared senior authorship.
• Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: Current state of knowledge. Cancer Treat Rev. (2013).
• Petersen K, Rajcevic U, Abdul Rahim SA, Jonassen I, Kalland KH, Jimenez CR, Bjerkvig R, Niclou SP. Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model. PLoS One 8(7):e68288 (2013).
• Emmink BL, Verheem A, Van Houdt WJ, Steller EJ, Govaert KM, Pham TV, Piersma SR, Borel Rinkes IH, Jimenez CR*, Kranenburg O*. The secretome of colon cancer stem cells contains drug-metabolizing enzymes. J Proteomics 91C:84-96 (2013). *Shared senior authorship.
• De Vries-van Leeuwen IJ, da Costa Pereira D, Flach KD, Piersma SR, Haase C, Bier D, Yalcin Z, Michalides R, Feenstra KA, Jiménez CR, de Greef TF, Brunsveld L, Ottmann C, Zwart W, de Boer AH. Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface. Proc Natl Acad Sci U S A 110(22):8894-9 (2013).
• Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jiménez CR. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci. 11(1):17 (2013).
• van der Woude AD, Mahendran KR, Ummels R, Piersma SR, Pham TV, Jiménez CR, de Punder K, van der Wel NN, Winterhalter M, Luirink J, Bitter W, Houben EN. Differential detergent extraction of mycobacterium marinum cell envelope proteins identifies an extensively modified threonine-rich outer membrane protein with channel activity. J Bacteriol. 195(9):2050-9 (2013).
• Warmoes M, Jaspers JE, Xu G, Sampadi BK, Pham TV, Knol JC, Piersma SR, Boven E, Jonkers J, Rottenberg S*, Jimenez CR*. Proteomics of genetically engineered mouse mammary tumors identifies fatty acid metabolism members as potential predictive markers for cisplatin resistance. Mol Cell Proteomics 12(5):1319-34 (2013). *Shared senior authorship.
• Schaaij-Visser TB, de Wit M, Lam SW, Jiménez CR. The cancer secretome, current status and opportunities in the lung, breast and colorectal cancer context. Biochim Biophys Acta. (2013). doi:pii: S1570-9639(13)00040-X. 10.1016/j.bbapap.2013.01.029.
• Albrethsen J, Agner J, Piersma SR, Højrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P, Rosenkrands I. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems. Mol Cell Proteomics 12(5):1180-91 (2013).
• de Wit M, Fijneman RJA, Verheul HMW, Meijer GA, Jimenez CR. Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin Biochem. 46(6):466-79 (2013).

2012

• Pham TV, Jimenez CR. An accurate paired sample test for count data. Bioinformatics 28(18):i596-i602 (2012).
• Houben EN, Bestebroer J, Ummels R, Wilson L, Piersma SR, Jiménez CR, Ottenhoff TH, Luirink J, Bitter W. Composition of the type VII secretion system membrane complex. Mol Microbiol. 86(2):472-84 (2012).
• Daleke MH, van der Woude AD, Parret AH, Ummels R, de Groot AM, Watson D, Piersma SR, Jiménez CR, Luirink J, Bitter W, Houben EN. Specific Chaperones for the Type VII Protein Secretion Pathway. J Biol Chem 287(38):31939-47 (2012).
• Kranenburg O, Emmink BL, Knol J, van Houdt WJ, Rinkes IH, Jimenez CR. Proteomics in studying cancer stem cell biology. Expert Rev Proteomics 9(3):325-36 (2012).
• Bogels M, Braster R, Nijland PG, Gul N, van de Luijtgaarden W, Fijneman RJA, Meijer GA, Jimenez CR, Beelen RHJ, van Egmond M. Carcinoma origin dictates differential skewing of monocyte function. OncoImmunology 1(7): 1-12 (2012).
• Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Reviews Mol. Diagnostics 12(4): 343-359 (2012).
• Fijneman RJ, de Wit M, Pourghiasian M, Piersma SR, Pham TV, Warmoes MO, Lavaei M, Piso C, Smit F, Delis-van Diemen PM, van Turenhout ST, Terhaar Sive Droste JS, Mulder CJ, Blankenstein MA, Robanus-Maandag EC, Smits R, Fodde R, van Hinsbergh VW, Meijer GA and Jimenez CR. Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer. Clin. Cancer Res. 18(9): 2613-2624 (2012).
• van Dijk KD, Berendse HW, Drukarch B, Fratantoni SA, Pham TV, Piersma SR, Huisman E, Brevé JJP, Groenewegen HJ, Jimenez CR*, van de Berg WDJ*. The proteome of the locus ceruleus in Parkinson’s disease: relevance to pathogenesis. Brain Pathol. 22(4):485-98 (2012).
• Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MP, Waisfisz Q, Rottenberg S, Boven E, Jonkers J and Jimenez CR. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with diagnostic and prognostic value in human breast cancer. Mol. Cell Proteomics 11: M111.013334 (2012).
• de Wit M, Jimenez CR, Carvalho B, Belien JA, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Pontén F, Meijer GA, Fijneman RJ. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut 61(6):855-64 (2012).

2011

• Bosch LJ, Carvalho B, Fijneman RJ, Jimenez CR, Pinedo HM, van EM and Meijer GA. Molecular tests for colorectal cancer screening. Clin. Colorectal Cancer 10: 8-23 (2011).
• Emmink BL, Van Houdt WJ, Vries RG, Hoogwater FJ, Govaert KM, Verheem A, Nijkamp MW, Steller EJ, Jimenez CR, Clevers H, Borel Rinkes IH and Kranenburg O. Differentiated human colorectal cancer cells protect tumor-initiating cells from irinotecan. Gastroenterology 141: 269-278 (2011).
• Gast MC, Zapatka M, van TH, Bontenbal M, Span PN, Tjan-Heijnen VC, Knol JC, Jimenez CR, Schellens JH and Beijnen JH. Postoperative serum proteomic profiles may predict recurrence-free survival in high-risk primary breast cancer. J. Cancer Res. Clin. Oncol. 137: 1773-1783 (2011).
• Knol JC and Jimenez CR. MALDI-TOF serum profiling using semiautomated serum peptide capture with magnetic reversed phase (C18) beads. Methods Mol. Biol. 790: 3-16 (2011).
• Skvortsov S, Jimenez CR, Knol JC, Eichberger P, Schiestl B, Debbage P, Skvortsova I and Lukas P. Radioresistant head and neck squamous cell carcinoma cells: intracellular signaling, putative biomarkers for tumor recurrences and possible therapeutic targets. Radiother. Oncol. 101: 177-182 (2011).
• Teunissen CE, Koel-Simmelink MJ, Pham TV, Knol JC, Khalil M, Trentini A, Killestein J, Nielsen J, Vrenken H, Popescu V, Dijkstra CD and Jimenez CR. Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult. Scler. 17: 838-850 (2011).
• Teunissen CE, Tumani H, Bennett JL, Berven FS, Brundin L, Comabella M, Franciotta D, Federiksen JL, Fleming JO, Furlan R, Hintzen RQ, Hughes SG, Jimenez CR, Johnson MH, Killestein J, Krasulova E, Kuhle J, Magnone MC, Petzold A, Rajda C, Rejdak K, Schmidt HK, van P, V, Waubant E, Wolf C, Deisenhammer F, Giovannoni G and Hemmer B. Consensus Guidelines for CSF and Blood Biobanking for CNS Biomarker Studies. Mult. Scler. Int. 2011: 246412 (2011).
• van Dijk KD, Berendse HW, Drukarch B, Fratantoni SA, Pham TV, Piersma SR, Huisman E, Breve JJ, Groenewegen HJ, Jimenez CR and van de Berg WD. The Proteome of the Locus Ceruleus in Parkinson’s Disease: Relevance to Pathogenesis. Brain Pathol. (2011).
• Van Houdt WJ, Emmink BL, Pham TV, Piersma SR, Verheem A, Vries RG, Fratantoni SA, Pronk A, Clevers H, Borel Rinkes IH, Jimenez CR and Kranenburg O. Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target. Mol. Cell Proteomics. 10: M111 (2011).

2010

• Albrethsen J, Knol JC, Piersma SR, Pham TV, de Wit M, Mongera S, Carvalho B, Verheul HM, Fijneman RJ, Meijer GA and Jimenez CR. Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol. Cell Proteomics. 9: 988-1005 (2010).
• Fratantoni SA, Piersma SR and Jimenez CR. Comparison of the performance of two affinity depletion spin filters for quantitative proteomics of CSF: Evaluation of sensitivity and reproducibility of CSF analysis using GeLC-MS/MS and spectral counting. Proteomics. Clin. Appl. 4: 613-617 (2010).
• Jimenez CR, Knol JC, Meijer GA and Fijneman RJ. Proteomics of colorectal cancer: overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers. J. Proteomics. 73: 1873-1895 (2010).
• Jimenez CR and Slijper M. Current status of cancer proteomics, how far are we from clinical applications? J. Proteomics. 73: 1787-1789 (2010).
• Pham TV, Piersma SR, Warmoes M and Jimenez CR. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics. 26: 363-369 (2010).
• Piersma SR, Labots M, Verheul HM and Jimenez CR. Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods. Anal. Bioanal. Chem. 397: 3163-3171 (2010).
• Piersma SR, Fiedler U, Span S, Lingnau A, Pham TV, Hoffmann S, Kubbutat MH and Jimenez CR. Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. J. Proteome. Res. 9: 1913-1922 (2010).
• Sani M, Houben EN, Geurtsen J, Pierson J, de PK, van ZM, Wever B, Piersma SR, Jimenez CR, Daffe M, Appelmelk BJ, Bitter W, van der Wel N and Peters PJ. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS. Pathog. 6: e1000794 (2010).
• Saydam O, Senol O, Schaaij-Visser TB, Pham TV, Piersma SR, Stemmer-Rachamimov AO, Wurdinger T, Peerdeman SM and Jimenez CR. Comparative protein profiling reveals minichromosome maintenance (MCM) proteins as novel potential tumor markers for meningiomas. J. Proteome. Res. 9: 485-494 (2010).
• Spitzer P, Klafki HW, Blennow K, Buee L, Esselmann H, Herruka SK, Jimenez C, Klivenyi P, Lewczuk P, Maler JM, Markus K, Meyer HE, Morris C, Muller T, Otto M, Parnetti L, Soininen H, Schraen S, Teunissen C, Vecsei L, Zetterberg H and Wiltfang J. cNEUPRO: Novel Biomarkers for Neurodegenerative Diseases. Int. J. Alzheimers. Dis. 2010: (2010).
• van Dijk KD, Teunissen CE, Drukarch B, Jimenez CR, Groenewegen HJ, Berendse HW and van de Berg WD. Diagnostic cerebrospinal fluid biomarkers for Parkinson’s disease: a pathogenetically based approach. Neurobiol. Dis. 39: 229-241 (2010).

2009

• Abdallah AM, Verboom T, Weerdenburg EM, Gey van Pittius NC, Mahasha PW, Jimenez C, Parra M, Cadieux N, Brennan MJ, Appelmelk BJ and Bitter W. PPE and PE_PGRS proteins of Mycobacterium marinum are transported via the type VII secretion system ESX-5. Mol. Microbiol. 73: 329-340 (2009).
• Albrethsen J, Knol JC and Jimenez CR. Unravelling the nuclear matrix proteome. J. Proteomics. 72: 71-81 (2009).
• Checinska A, Giaccone G, Rodriguez JA, Kruyt FA and Jimenez CR. Comparative proteomics analysis of caspase-9-protein complexes in untreated and cytochrome c/dATP stimulated lysates of NSCLC cells. J. Proteomics. 72: 575-585 (2009).
• Gast MC, van Dulken EJ, van Loenen TK, Kingma-Vegter F, Westerga J, Flohil CC, Knol JC, Jimenez CR, van Gils CH, Wessels LF, Schellens JH and Beijnen JH. Detection of breast cancer by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry tissue and serum protein profiling. Int. J. Biol. Markers 24: 130-141 (2009).
• Jimenez CR. Sorting and zooming: subcellular proteomics is booming! J. Proteomics. 72: 1-3 (2009).
• Piersma SR, Broxterman HJ, Kapci M, de Haas RR, Hoekman K, Verheul HM and Jimenez CR. Proteomics of the TRAP-induced platelet releasate. J. Proteomics. 72: 91-109 (2009).
• Rajcevic U, Niclou SP and Jimenez CR. Proteomics strategies for target identification and biomarker discovery in cancer. Front Biosci. 14: 3292-3303 (2009).
• Rajcevic U, Petersen K, Knol JC, Loos M, Bougnaud S, Klychnikov O, Li KW, Pham TV, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez CR and Niclou SP. iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol. Cell Proteomics. 8: 2595-2612 (2009).
• Tefsen B, van Stijn CM, van den Broek M, Kalay H, Knol JC, Jimenez CR and van D, I. Chemoenzymatic synthesis of multivalent neoglycoconjugates carrying the helminth glycan antigen LDNF. Carbohydr. Res. 344: 1501-1507 (2009).
• van Dijk FS, Nesbitt IM, Zwikstra EH, Nikkels PG, Piersma SR, Fratantoni SA, Jimenez CR, Huizer M, Morsman AC, Cobben JM, van Roij MH, Elting MW, Verbeke JI, Wijnaendts LC, Shaw NJ, Hogler W, McKeown C, Sistermans EA, Dalton A, Meijers-Heijboer H and Pals G. PPIB mutations cause severe osteogenesis imperfecta. Am. J. Hum. Genet. 85: 521-527 (2009).
• Voortman J, Pham TV, Knol JC, Giaccone G and Jimenez CR. Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profiling. Proteome. Sci. 7: 34 (2009).

2008

• Engwegen JY, Alberts M, Knol JC, Jimenez CR, Depla AC, Tuynman H, van Heukelem HA, Snel P, Smits ME, Cats A, Schellens JH and Beijnen JH. Influence of variations in sample handling on SELDI-TOF MS serum protein profiles for colorectal cancer. Proteomics. Clin. Appl. 2: 936-945 (2008).
• Hamacher M, Stephan C, Hardt T, Eisenacher M, Henkel A, Wiltfang J, Jimenez CR, Park YM, Marcus K and Meyer HE. Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea. Proteomics. 8: 1750-1753 (2008).
• Jimenez CR. Mass spectrometry-based proteomics: trends in tools and strategies. Eur. Pharm. Rev. 2008: 24-25 (2008).
• Li KW and Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert. Rev. Proteomics. 5: 353-360 (2008).
• Pham TV, van de Wiel MA and Jimenez CR. Support vector machine approach to separate control and breast cancer serum samples. Stat. Appl. Genet. Mol. Biol. 7: Article11 (2008).
• Pham TV and Jimenez CR. OplAnalyzer: a toolbox for MALDI-TOF mass spectrometry data analysis. In: Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry, Third International Conference, MDA 2008, Leipzig, Germany, Proceedings Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 5108: 73-81 (2008).

2007

• Jiménez CR. Mass spectrometry-based proteomics: trends in tools and strategies. Eur. Pharm. Revs. p24-25 (2007).
• Codrea MC, Jimenez CR, Piersma S, Heringa J and Marchiori E. Robust peak detection and alignment of nanoLC-FT mass spectrometry data. In: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 5th European Conference, EvoBIO 2007, Valencia, Spain, Proceedings (Marchiori E, Moore JH and Rajapakse JC, eds.), Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 4447: 35-46 (2007).
• Codrea MC, Jimenez CR, Heringa J and Marchiori E. Tools for computational processing of LC-MS datasets: a user’s perspective. Comput. Methods Programs Biomed. 86: 281-290 (2007).
• Jimenez CR, Piersma S and Pham TV. High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery. Biomark. Med. 1: 541-565 (2007).
• Jimenez CR, El FZ, Knol JC, Hoekman K, Kruyt FA, Giaccone G, Smit AB and Li KW. Automated serum peptide profiling using novel magnetic C18 beads off-line coupled to MALDI-TOF-MS. Proteomics. Clin. Appl. 1: 598-604 (2007).
• Jimenez CR, Koel-Simmelink M, Pham TV, van d, V and Teunissen CE. Endogeneous peptide profiling of cerebrospinal fluid by MALDI-TOF mass spectrometry: Optimization of magnetic bead-based peptide capture and analysis of preanalytical variables. Proteomics. Clin. Appl. 1: 1385-1392 (2007).

2006

• Eiras S, Narolska NA, van Loon RB, Boontje NM, Zaremba R, Jimenez CR, Visser FC, Stooker W, van d, V and Stienen GJ. Alterations in contractile protein composition and function in human atrial dilatation and atrial fibrillation. J. Mol. Cell Cardiol. 41: 467-477 (2006).
• Llamas MA, Sparrius M, Kloet R, Jimenez CR, Vandenbroucke-Grauls C and Bitter W. The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J. Bacteriol. 188: 1882-1891 (2006).
• Marchiori E, Jimenez CR, West-Nielsen M and Heegaard N. Robust SVM-based biomarker selection with noisy mass spectrometric proteomic data. In: Applications of Evolutionary Computing: EvoBIO, Fourth European Workshop on Evolutionary Bioinformatics, Budapest, Hungary, Proceedings (Rothlauf F, Branke J, Cagnoni S, Costa E, Cotta R, Drechsler R, Lutton E, Machado P, Moore JH, Romero J, Smith GD, Squillero G and Takagi H, eds.), Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 3907: 79-90 (2006).
• Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse C, Geraerts WPM, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li KW. Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability. J. Neurosci. 26:518-529 (2006).
• Li KW, Jiménez CR, Hornshaw MP, Van der Schors RC, Schoffelmeer ANM, Smit AB. Intermittent administration of morphine alters protein expression in rat nucleus accumbens. Proteomics 6(6)(2006).
• Van den Oever MC, Spijker S, Li KW, Jiménez CR, Koya E, Van der Schors RC, Gouwenberg Y, Binnekade R, De Vries TJ, Schoffelmeer ANM, Smit AB. A proteomics approach to identify long-term molecular changes in rat medial prefrontal cortex resulting from sucrose self-administration. J. Prot. Res. 5:147-154 (2006).