A correction was made to: Protein Complex Affinity Capture from Cryomilled Mammalian Cells. The References section has been updated from:
- Cristea, I. M., & Chait, B. T. Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harbor Protocols. 2011 (5) (2011).
- Rosenberg, I. M. Electrophoretic Techniques. Protein Analysis and Purification. (4), 63–117 (2005).
- Ornstein, L. Disc Electrophoresis. I. Background and Theory. Ann N Y Acad Sci. 121 (A2), 321–349 (1964).
- Davis, B. J. Disc Electrophoresis. II. Method and Application to Human Serum Proteins. Ann N Y Acad Sci. 121, 404–427 (1964).
- Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227 (5259), 680–685 (1970).
- Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature protocols. 1 (6), 2856–2860 (2006).
- DeGrasse, J. A., Kalkum, M., Krutchinsky, A.N., Padovan, J. C., & Zhang, W. MALDI Sample Preparation. rockefeller.edu at <http://prowl.rockefeller.edu/protocols/in-gel-digestion.html> (2006).
- Lubas, M., Christensen, M. S., et al. Interaction profiling identifies the human nuclear exosome targeting complex. Mol Cell. 43 (4), 624–637 (2011).
- Tackett, A. J., DeGrasse, J. A., Sekedat, M. D., Oeffinger, M., Rout, M. P., & Chait, B. T. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res. 4 (5), 1752–1756 (2005).
- Wang, X., & Huang, L. Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Mol Cell Proteomics. 7 (1), 46–57 (2008).
- Trinkle-Mulcahy, L., Boulon, S., et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol. 183 (2), 223–239 (2008).
- Boulon, S., Ahmad, Y., et al. Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol Cell Proteomics. 9 (5), 861–879 (2010).
- Armean, I. M., Lilley, K. S., & Trotter, M. W. B. Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics. 12 (1), 1–13 (2013).
- Mellacheruvu, D., Wright, Z., et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. (2013).
- Cheeseman, I. M., & Desai, A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE 2005 (266), pl1 (2005).
- Goldberg, S. Mechanical/physical methods of cell disruption and tissue homogenization. Methods in Molecular Biology. 424 (Chapter 1), 3–22 (2008).
- Grabski, A. C. Advances in preparation of biological extracts for protein purification. Methods in Enzymology. 463 (C), 285–303 (2009).
- Dhabaria, A., Cifani, P., Reed, C., Steen, H., & Kentsis, A. A High-Efficiency Cellular Extraction System for Biological Proteomics. J Proteome Res. 14 (8), 3403–3408 (2015).
- Glatter, T., Ahrné, E., & Schmidt, A. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res. 15 (2), 679 (2016).
- Zhao, Q.-Q., Yamada, S., & Jimbo, G. The Mechanism and Grinding Limit of Planetary Ball Milling. KONA. 7, 29–36 (1989).
- Sheng-Yong, L., Qiong-Jing, M., Zheng, P., Xiao-Dong, L., & Jian-Hua, Y. Simulation of ball motion and energy transfer in a planetary ball mill. Chinese Phys. B 21 (7), 078201 (2012).
- Fulton, A. B. How crowded is the cytoplasm? Cell. 30 (2), 345–347 (1982).
- Ellis, R. J. Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. 26 (10), 597–604 (2001).
- Kalkum, M. Using the Retsch MM301 Ball Mill for Cryogenic Disruption of Yeast Cells. 2 City of Hope, (2003).
- Staley, J. Making Whole Cell Extract of Saccharomyces cerevisiae cells using the Retsch MM301 Ball Mill. Retsch GmbH: (2005).
- Bell, A. W., Nilsson, T., Kearney, R. E., & Bergeron, J. J. M. The protein microscope: Incorporating mass spectrometry into cell biology. Nat Methods. 4 (10), 783–784 (2007).
- Zhao, X., Li, G., & Liang, S. Several affinity tags commonly used in chromatographic purification. J Anal Methods Chem. 2013 (1), 581093–8 (2013).
- Waugh, D. S. An overview of enzymatic reagents for the removal of affinity tags. 80 (2), 283–293 (2011).
- Williams, R. J., & Lyman, C. M. A neutral buffered standard for hydrogen ion work and accurate titrations which can be prepared in one minute. J Am Chem Soc. 54 (5), 1911–1912 (1932).
- Johnson, M. Detergents: Triton X-100, Tween-20, and More. labome.com. 3 (163) (2013).
- Deppert, W. R., & Lukaĉin, R. Buffers and Additives. Journal of Chromatography Library. 61 (C), 839–862 (1999).
- Ugwu, S. O., & Apte, S. P. The Effect of Buffers on Protein Conformational Stability. Pharmaceutical Technology. 28 (3), 86–108 (2004).
- Linke, D. Detergents: an overview. Methods in Enzymology. 463 (34), 603–617 (2009).
- Zhang, J. Protein-Protein Interactions in Salt Solutions. Protein-Protein Interactions Computational and Experimental Tools. (18), 359–376 (2012).
to:
- Ball Mills - Guidelines for sample amount and ball charge. 1–3at <http://www.retsch.com/products/milling/ball-mills/planetary-ball-mill-pm-100/information-downloads/> Retsch GmbH (2014).
- Cristea, I. M., & Chait, B. T. Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harbor Protocols. 2011 (5) (2011).
- Rosenberg, I. M. Electrophoretic Techniques. Protein Analysis and Purification. (4), 63–117 (2005).
- Ornstein, L. Disc Electrophoresis. I. Background and Theory. Ann N Y Acad Sci. 121 (A2), 321–349 (1964).
- Davis, B. J. Disc Electrophoresis. II. Method and Application to Human Serum Proteins. Ann N Y Acad Sci. 121, 404–427 (1964).
- Laemmli, U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 227 (5259), 680–685 (1970).
- Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., & Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nature protocols. 1 (6), 2856–2860 (2006).
- DeGrasse, J. A., Kalkum, M., Krutchinsky, A.N., Padovan, J. C., & Zhang, W. MALDI Sample Preparation. rockefeller.edu at <http://prowl.rockefeller.edu/protocols/in-gel-digestion.html> (2006).
- Lubas, M., Christensen, M. S., et al. Interaction profiling identifies the human nuclear exosome targeting complex. Mol Cell. 43 (4), 624–637 (2011).
- Tackett, A. J., DeGrasse, J. A., Sekedat, M. D., Oeffinger, M., Rout, M. P., & Chait, B. T. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res. 4 (5), 1752–1756 (2005).
- Wang, X., & Huang, L. Identifying dynamic interactors of protein complexes by quantitative mass spectrometry. Mol Cell Proteomics. 7 (1), 46–57 (2008).
- Trinkle-Mulcahy, L., Boulon, S., et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol. 183 (2), 223–239 (2008).
- Boulon, S., Ahmad, Y., et al. Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners. Mol Cell Proteomics. 9 (5), 861–879 (2010).
- Armean, I. M., Lilley, K. S., & Trotter, M. W. B. Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics. 12 (1), 1–13 (2013).
- Mellacheruvu, D., Wright, Z., et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods. (2013).
- Cheeseman, I. M., & Desai, A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE 2005 (266), pl1 (2005).
- Deppert, W. R., & Lukaĉin, R. Buffers and Additives. Journal of Chromatography Library. 61 (C), 839–862 (1999).
- Ugwu, S. O., & Apte, S. P. The Effect of Buffers on Protein Conformational Stability. Pharmaceutical Technology. 28 (3), 86–108 (2004).
- Linke, D. Detergents: an overview. Methods in Enzymology. 463 (34), 603–617 (2009).
- Zhang, J. Protein-Protein Interactions in Salt Solutions. Protein-Protein Interactions Computational and Experimental Tools. (18), 359–376 (2012).
- Goldberg, S. Mechanical/physical methods of cell disruption and tissue homogenization. Methods in Molecular Biology. 424 (Chapter 1), 3–22 (2008).
- Grabski, A. C. Advances in preparation of biological extracts for protein purification. Methods in Enzymology. 463 (C), 285–303 (2009).
- Dhabaria, A., Cifani, P., Reed, C., Steen, H., & Kentsis, A. A High-Efficiency Cellular Extraction System for Biological Proteomics. J Proteome Res. 14 (8), 3403–3408 (2015).
- Glatter, T., Ahrné, E., & Schmidt, A. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res. 15 (2), 679 (2016).
- Zhao, Q.-Q., Yamada, S., & Jimbo, G. The Mechanism and Grinding Limit of Planetary Ball Milling. KONA. 7, 29–36 (1989).
- Sheng-Yong, L., Qiong-Jing, M., Zheng, P., Xiao-Dong, L., & Jian-Hua, Y. Simulation of ball motion and energy transfer in a planetary ball mill. Chinese Phys. B 21 (7), 078201 (2012).
- Fulton, A. B. How crowded is the cytoplasm? Cell. 30 (2), 345–347 (1982).
- Ellis, R. J. Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. 26 (10), 597–604 (2001).
- Kalkum, M. Using the Retsch MM301 Ball Mill for Cryogenic Disruption of Yeast Cells. 2 City of Hope, (2003).
- Staley, J. Making Whole Cell Extract of Saccharomyces cerevisiae cells using the Retsch MM301 Ball Mill. Retsch GmbH: (2005).
- Bell, A. W., Nilsson, T., Kearney, R. E., & Bergeron, J. J. M. The protein microscope: Incorporating mass spectrometry into cell biology. Nat Methods. 4 (10), 783–784 (2007).
- Zhao, X., Li, G., & Liang, S. Several affinity tags commonly used in chromatographic purification. J Anal Methods Chem. 2013 (1), 581093–8 (2013).
- Waugh, D. S. An overview of enzymatic reagents for the removal of affinity tags. 80 (2), 283–293 (2011).