B. Y.  Renard, Xu, B., Kirchner, M., Zickmann, F., Winter, D., Korten, S., Brattig, N., Tzur, A., Hamprecht, F. A., and Steen, H., ?Overcoming species boundaries in peptide identification with BICEPS?, Molecular and Cellular Proteomics, vol. 11, 2012.

M.  Hanselmann, Voss, B., Renard, B. Y., Lindner, M., Köthe, U., Kirchner, M., and Hamprecht, F. A., ?SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists?, Bioinformatics, vol. 27 (7), pp. 987-993, 2011.

A.  Kreshuk, Stankiewicz, M., Lou, X., Kirchner, M., Hamprecht, F. A., and Mayer, M. P., ?Automated detection and analysis of bimodal isotope peak distribution in H/D exchange mass spectrometry using HeXicon?, International Journal of Mass Spectrometry, vol. 302, pp. 125-131, 2010.

M.  Kirchner, Renard, B. Y., Köthe, U., Pappin, D. J., Hamprecht, F. A., Steen, J. A. J., and Steen, H., ?Computational Protein Profile Similarity Screening for Quantitative Mass Spectrometry Experiments?, Bioinformatics, vol. 26 (1), pp. 77-83, 2010.

X.  Lou, Kirchner, M., Renard, B. Y., Köthe, U., Graf, C., Lee, C., Steen, J. A. J., Steen, H., Mayer, M. P., and Hamprecht, F. A., ?Deuteration Distribution Estimation with Improved Sequence Coverage for HX/MS Experiments?, Bioinformatics, vol. 26(12), pp. 1535-1541, 2010.

B. Y.  Renard, Timm, W., Kirchner, M., Steen, J. A. J., Hamprecht, F. A., and Steen, H., ?Estimating the Confidence of Peptide Identifications without Decoy Databases?, Analytical Chemistry, pp. 4314-4318, 2010.

M.  Kirchner, Steen, J. A. J., Hamprecht, F. A., and Steen, H., ?MGFp: An Open Mascot Generic Format Parser Library Implementation?, Journal of Proteome Research, vol. 9 (5), p. 27622763, 2010.

M.  Hanselmann, Köthe, U., Renard, B. Y., Kirchner, M., Heeren, R. M. A., and Hamprecht, F. A., ?Multivariate Watershed Segmentation of Compositional Data?, in Proceedings of the 15th International Conference on Discrete Geometry for Computer Imagery (DGCI), in press, 2009, vol. 5810, pp. 180-192.

M.  Hanselmann, Köthe, U., Kirchner, M., Renard, B. Y., Amstalden, E. R., Glunde, K., Heeren, R. M. A., and Hamprecht, F. A., ?Towards Digital Staining using Imaging Mass Spectrometry and Random Forests?, Journal of Proteome Research, vol. 8, pp. 3558-3567, 2009.

B. Y.  Renard, Kirchner, M., Monigatti, F., Ivanov, A. R., Rappsilber, J., Winter, D., Steen, J. A. J., Hamprecht, F. A., and Steen, H., ?When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification Preprocessing?, Proteomics, vol. 9, pp. 4978-4984, 2009.

M.  Kirchner, ?Analysis of Spectral Data?. University of Heidelberg, 2008.

M.  Hanselmann, Kirchner, M., Renard, B. Y., Amstalden, E. R., Glunde, K., Heeren, R. M. A., and Hamprecht, F. A., ?Concise Representation of MS Images by Probabilistic Latent Semantic Analysis?, Analytical Chemistry, vol. 80, pp. 9649-9658, 2008.

J. A. J.  Steen, Steen, H., Georgi, A., Parker, K. C., Springer, M., Kirchner, M., Hamprecht, F. A., and Kirschner, M. W., ?Different Phosphorylation States of the Anaphase Promoting Complex in Response to Anti-Mitotic Drugs: A Quantitative Proteomic Analysis?, Proceedings of the National Academy of Sciences, vol. 105, pp. 6069-6074, 2008.

B. Y.  Renard, Kirchner, M., Steen, H., Steen, J. A. J., and Hamprecht, F. A., ?NITPICK: Peak Identification for Mass Spectrometry Data?, BMC Bioinformatics, vol. 9, p. 355, 2008.

T.  König, Menze, B. H., Kirchner, M., Monigatti, F., Parker, K. C., Patterson, T., Steen, J. J., Hamprecht, F. A., and Steen, H., ?Robust Prediction of the MASCOT Score for an Improved Quality Assessment in Mass Spectrometric Proteomics?, Journal of Proteome Research, vol. 7, pp. 3708-3717, 2008.

M.  Kirchner, Saussen, B., Steen, H., Steen, J. A. J., and Hamprecht, F. A., ?amsrpm: Robust Point Matching in Retention Time Alignment of LC/MS Data with R?, Journal of Statistical Software, vol. 18, pp. 1-12, 2007.

M.  Kirchner, ?Spatial extensions to self-modeling curve resolution?, University of Heidelberg, 2004.