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.

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.

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.

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.