The Bioinformatics group uses computational tools to bring together data from different domains in order to better understand human disease. The group develops and operates advanced mass spectrometry instrumentation, such as an FTICR-ion trap cluster, for large-scale and label-free proteomics data. This system was used to produce the first population-based proteomics study, linking the plasma protein abundance (phenotype) to genotypic variability. We also optimize design-of-experiment, by using scientific workflows to integrate all available resources and information, including mass spectral libraries to select the best surrogate peptides for targeted, labeled, quantitative proteomics. This is both a research method and a technique eminently amenable to routine application in clinical labs. We have pioneered direct spectral comparison techniques for molecular phylogenetics and the similar use of spectral libraries to differentiate and identify biological samples, including important human pathogens. We also use model systems such as mouse, and in particular zebrafish, to study infectious diseases and cancer in collaboration with several groups within the LUMC and at Leiden University.
Our software is used by many groups worldwide, and our spectral libraries included in the NIST high-quality spectral library collection. We strive to always be ahead of the rapidly changing and improving instrumentation with simulation and analyzing massive amounts of data acquired in our and other researchers’ labs. We publish our work in leading journals in the field, including Molecular and Cellular Proteomics, Journal of Proteome Research, Analytical Chemistry and Journal of Proteomics, but also general journals such as P.N.A.S. We also mine the scientific literature using advanced, scientific workflow-based, bibliometric methods.
Mohammed Y, Bhowmick P, Smith DS, Domański D, Jackson AM, Michaud SA, Malchow S, Percy AJ, Chambers AG, Palmer A, Zhang S, Sickmann A, Borchers CH. PeptideTracker: A knowledgebase for collecting and storing information on protein concentrations in biological tissues. Proteomics 2016 Sep 29. PMID: 27683069
Kolder IC, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT, Travin DY, Nakao M, Moritomo T, Irnazarow I, den Dunnen JT, Anvar SY, Jansen HJ, Dirks RP, Palmblad M, Lenhard B, Henkel CV, Spaink HP. A full-body transcriptome and proteome resource for the European common carp. BMC genomics 2016 Sep 2; ;17(1):701 PMID: 27590662
Nessen MA, van der Zwaan DJ, Grevers S, Dalebout H, Staats M, Kok E, Palmblad M. Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching. Journal of agricultural and food chemistry 2016 May 11;64(18):3669-77 PMID: 27086584
Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L. A Pipeline for Differential Proteomics in Unsequenced Species. Journal of proteome research 2016 May 2; Pubmed PMID: 27089233
Plas-Duivesteijn SJ, Wulff T, Klychnikov O, Ohana D, Dalebout H, van Veelen PA, de Keijzer J, Nessen MA, van der Burgt YE, Deelder AM, Palmblad M. Differentiating samples and experimental protocols by direct comparison of tandem mass spectra. Rapid communications in mass spectrometry : RCM 2016 Mar 30;30(6):731-8 PMID: 26864526
Guler AT, Waaijer CJ, Palmblad M. Scientific workflows for bibliometrics. Scientometrics. 2016;107:385-398. Epub 2016 Feb 15. Pubmed PMID: 27122644
Muller C, Yassin K, Li LS, Palmblad M, Efendic S, Berggren PO, Cerami A, Brines M, Östenson CG. ARA290 improves insulin release and glucose tolerance in type 2 diabetic GK rats. Mol Med. 2015 Dec 29. doi: 10.2119/molmed.2015.00267. PubMed PMID: 26736179
Holl S, Mohammed Y, Zimmermann O, Palmblad M. Scientific workflow optimization for improved peptide and protein identification. BMC Bioinformatics. 2015 Sep 3;16:284. doi: 10.1186/s12859-015-0714-x. PubMed PMID: 26335531
Mohammed Y, Borchers CH. An extensive library of surrogate peptides for all human proteins. J Proteomics. 2015 Nov 3;129:93-7. doi: 10.1016/j.jprot.2015.07.025. Epub 2015 Jul 29. PubMed PMID: 26232110
Ohana D, Dalebout H, Marissen RJ, Wulff T, Bergquist J, Deelder AM, Palmblad M. Identification of meat products by shotgun spectral matching. Food chemistry 2016 Jul 15;203:28-34 PMID: 26948585
de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, ‘t Hoen PA. Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res. 2015 May 19;43(9):4408-28. doi: 10.1093/nar/gkv281. Epub 2015 Apr 14. PubMed PMID: 25873627
Waaijer CJ, Palmblad M. Bibliometric mapping: eight decades of analytical chemistry, with special focus on the use of mass spectrometry. Anal Chem. 2015;87(9):4588-96. doi: 10.1021/ac5040314. Epub 2015 Mar 26. Pubmed PMID: 25745805
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