**Author details**

Jakub Faktor1 , David R. Goodlett1,2,3 and Irena Dapic1 \*

1 International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland

2 Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada

3 University of Victoria Genome BC Proteome Centre, Victoria, BC, Canada

\*Address all correspondence to: irena.dapic@ug.edu.pl

© 2021 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**23**

*Trends in Sample Preparation for Proteome Analysis DOI: http://dx.doi.org/10.5772/intechopen.95962*

> peptide identification with MS-based proteomics', Mol. Biosyst., vol. 13, no. 12, pp. 2574-2582, Nov. 2017, doi:

[9] Y. Zhu et al., 'High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification', Mol. Oncol., vol. 13, no. 11, pp. 2305-2328, 2019, doi: 10.1002/1878-0261.12570.

[10] J. R. Wiśniewski, C. Wegler, and P. Artursson, 'Multiple-Enzyme-Digestion

Strategy Improves Accuracy and Sensitivity of Label- and Standard-Free Absolute Quantification to a Level That Is Achievable by Analysis with Stable Isotope-Labeled Standard Spiking', J. Proteome Res., vol. 18, no. 1, pp. 217-224, 04 2019, doi: 10.1021/acs.

[11] N. Taouatas, S. Mohammed, and A. J. R. Heck, 'Exploring new proteome space: combining Lys-N proteolytic digestion and strong cation exchange (SCX) separation in peptide-centric MS-driven proteomics', Methods Mol. Biol. Clifton NJ, vol. 753, pp. 157-167, 2011, doi: 10.1007/978-1-61779-148-2\_11.

[12] R. G. Biringer, H. Amato, M. G. Harrington, A. N. Fonteh, J. N. Riggins,

sequence coverage of proteins in human cerebrospinal fluid using multiple enzymatic digestion and linear ion trap LC-MS/MS', Brief. Funct. Genomic. Proteomic., vol. 5, no. 2, pp. 144-153, Jun. 2006, doi: 10.1093/bfgp/ell026.

[13] R. Chen et al., 'Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry', J. Proteome Res., vol. 8, no. 2, pp. 651-661, Feb. 2009, doi: 10.1021/pr8008012.

[14] J. R. Wiśniewski and M. Mann, 'Consecutive proteolytic digestion in

and A. F. R. Hühmer, 'Enhanced

jproteome.8b00549.

10.1039/c7mb00393e.

[1] M. M. Morente et al., 'TuBaFrost 2: Standardising tissue collection and quality control procedures for a European virtual frozen tissue bank network', Eur. J. Cancer Oxf. Engl. 1990, vol. 42, no. 16, pp. 2684-2691, Nov. 2006, doi: 10.1016/j.ejca.2006.04.029.

[2] S. R. Mager et al., 'Standard operating procedure for the collection of fresh frozen tissue samples', Eur. J. Cancer Oxf. Engl. 1990, vol. 43, no. 5, pp. 828-834, Mar. 2007, doi: 10.1016/j.ejca.2007.01.002.

[3] H. Meng et al., 'Tissue triage and freezing for models of skeletal muscle disease', J. Vis. Exp. JoVE, no. 89, Jul.

[4] B. Enthaler, T. Bussmann, J. K. Pruns, C. Rapp, M. Fischer, and J.-P. Vietzke, 'Influence of various on-tissue washing procedures on the entire protein quantity and the quality of matrixassisted laser desorption/ionization spectra', Rapid Commun. Mass Spectrom. RCM, vol. 27, no. 8, pp. 878- 884, Apr. 2013, doi: 10.1002/rcm.6513.

2014, doi: 10.3791/51586.

[5] L. Giusti and A. Lucacchini, 'Proteomic studies of formalin-fixed paraffin-embedded tissues', Expert Rev. Proteomics, vol. 10, no. 2, pp. 165-177, Apr. 2013, doi: 10.1586/epr.13.3.

[7] I. Rehman and S. Botelho, 'Biochemistry, Tertiary Structure, Protein', in StatPearls, Treasure Island (FL): StatPearls Publishing, 2020.

[8] S. Suttapitugsakul, H. Xiao, J. Smeekens, and R. Wu, 'Evaluation and optimization of reduction and alkylation methods to maximize

[6] E. I. Chen, D. Cociorva, J. L. Norris, and J. R. Yates, 'Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun Proteomics', J. Proteome Res., vol. 6, no. 7, pp. 2529-2538, Jul. 2007, doi: 10.1021/pr060682a.

**References**

*Trends in Sample Preparation for Proteome Analysis DOI: http://dx.doi.org/10.5772/intechopen.95962*
