TY - JOUR AU - Choi, H. AU - Fermin, D. AU - Nesvizhskii, A. I. PY - 2008 DA - 2008// TI - Significance analysis of spectral count data in label-free shotgun proteomics JO - Mol Cell Proteomics VL - 7 UR - https://doi.org/10.1074/mcp.M800203-MCP200 DO - 10.1074/mcp.M800203-MCP200 ID - Choi2008 ER - TY - JOUR AU - Wiese, S. AU - Reidegeld, K. A. AU - Meyer, H. E. AU - Warscheid, B. PY - 2007 DA - 2007// TI - Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research JO - Proteomics VL - 7 UR - https://doi.org/10.1002/pmic.200600422 DO - 10.1002/pmic.200600422 ID - Wiese2007 ER - TY - JOUR AU - Michalski, A. AU - Cox, J. AU - Mann, M. PY - 2011 DA - 2011// TI - More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Marjority is Inaccessible to Data-Dependent LC-MS/MS JO - Journal of Proteome Research VL - 10 UR - https://doi.org/10.1021/pr101060v DO - 10.1021/pr101060v ID - Michalski2011 ER - TY - JOUR AU - Cappadona, S. AU - Baker, P. R. AU - Cutillas, P. R. AU - Heck, A. J. AU - van Breukelen, B. PY - 2012 DA - 2012// TI - Current challenges in software solutions for mass spectrometry-based quantitative proteomics JO - Amino Acids VL - 43 UR - https://doi.org/10.1007/s00726-012-1289-8 DO - 10.1007/s00726-012-1289-8 ID - Cappadona2012 ER - TY - JOUR AU - Tautenhahn, R. AU - Bottcher, C. AU - Neumann, S. PY - 2008 DA - 2008// TI - Highly sensitive feature detection for high resolution LC/MS JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-504 DO - 10.1186/1471-2105-9-504 ID - Tautenhahn2008 ER - TY - JOUR AU - Pluskal, T. AU - Castillo, S. AU - Villar-Briones, A. AU - Oresic, M. PY - 2010 DA - 2010// TI - MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-395 DO - 10.1186/1471-2105-11-395 ID - Pluskal2010 ER - TY - CHAP AU - Conley, C. J. AU - Smith, R. AU - Torgrip, R. J. AU - Taylor, R. M. AU - Tautenhahn, R. AU - Prince, J. T. PY - 2014 DA - 2014// TI - Massifquant: open-source Kalman filter based XC-MS isotope trace feature detection BT - Bioinformatics ID - Conley2014 ER - TY - JOUR AU - Cox, J. AU - Mann, M. PY - 2008 DA - 2008// TI - MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification JO - Nature Biotechnology VL - 26 UR - https://doi.org/10.1038/nbt.1511 DO - 10.1038/nbt.1511 ID - Cox2008 ER - TY - CHAP AU - Weisser, H. AU - Nahnsen, S. AU - Grossmann, J. AU - Nilse, L. AU - Quandt, A. AU - Brauer, H. AU - Sturm, M. AU - Kenar, E. AU - Kohlbacher, O. AU - Aebersold, R. PY - 2013 DA - 2013// TI - An automated pipeline for high-throughput label-free quantitative proteomics BT - Journal of Proteome Research ID - Weisser2013 ER - TY - JOUR AU - Bellew, M. AU - Coram, M. AU - Fitzgibbon, M. AU - Igra, M. AU - Randolph, T. AU - Wang, P. AU - May, D. AU - Eng, J. AU - Fang, R. AU - Lin, C. PY - 2006 DA - 2006// TI - A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl276 DO - 10.1093/bioinformatics/btl276 ID - Bellew2006 ER - TY - CHAP AU - Smith, R. AU - Ventura, D. AU - Prince, J. T. PY - 2013 DA - 2013// TI - LC-MS Alignment in Theory and Practice: A Comprehensive Algorithmic Review BT - Briefings in Bioinformatics ID - Smith2013 ER - TY - JOUR AU - Listgarten, J. AU - Neal, R. M. AU - Roweis, S. T. AU - Wong, P. AU - Emili, A. PY - 2007 DA - 2007// TI - Difference detection in LC-MS data for protein biomarker discovery JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl326 DO - 10.1093/bioinformatics/btl326 ID - Listgarten2007 ER -