References
[1] Orsburn BC. Proteome Discoverer-A Community Enhanced Data Processing Suite for Protein Informatics. Proteomes. 2021 Mar 23; 9(1):15. doi: 10.3390/proteomes9010015.
[2] Chen C, Hou J, Tanner JJ, Cheng J. Bioinformatics methods for mass spectrometry-based proteomics data analysis. Int J Mol Sci. 2020; 21(8), 2873. https://doi.org/10.3390/ijms21082873
[3] Verheggen K, Ræder H, Berven FS, Martens L, Barsnes H, Vaudel M. Anatomy and evolution of database search engines - a central component of mass spectrometry based proteomic workflows. Mass Spectrom Rev. 2020; 39(3):292-306.
[4] Tsiamis V, Ienasescu HI, Gabrielaitis D, Palmblad M, Schwämmle V, Ison J. One Thousand and One Software for Proteomics: Tales of the Toolmakers of Science. J Proteome Res. 2019;18 (10):3580–5.
[5] Prakash A, Ahmad S, Majumder S, Jenkins C, Orsburn B. Bolt: a New Age Peptide Search Engine for Comprehensive MS/MS Sequencing Through Vast Protein Databases in Minutes. J Am Soc Mass Spectrom. 2019 Nov;30(11):2408-2418. doi: 10.1007/s13361-019-02306-3.
[6] Röst H L, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich H C, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary J S, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016; 13(9):741-8.
[7] Chen T, Zhao J, Ma J, Zhu Y. Web resources for mass spectrometry-based proteomics. Genomics, Proteomics Bioinformatics. 2015;13(1):36 - 39. doi:10.1016/j.gpb.2015.01.004.
[8] Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno J A. Open source libraries and frameworks for mass spectrometry based proteomics: A developer’s perspective. Biochim Biophys Acta - Proteins Proteomics 2014;1844 (1 Pt A):63-76.
doi: 10.1016/j.bbapap.2013.02.032. .
[9] Allmer J. Algorithms for the de novo sequencing of peptides from tandem mass spectra. Expert Rev Proteomics. 2011; 8:645-657.
[10] Cox J, Neuhauser N, Michalski A, Scheltema R A, Olsen J V, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res 2011; 10(4):1794-1805.
[11] Perkins D N, Pappin D J, Creasy D M, Cottrell J S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999; 20 (18): 3551-3567.
[12] Eng J K, McCormack A L,Yates J R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom 1994; 5:976-989.
[13] Zhang Y, Fonslow B R, Shan B, Baek M C, Yates J R 3rd. Protein analysis by shotgun/bottom-up proteomics. Chem Rev. 2013; 113 (4):2343-94.
[14] Gonzalez-Galarza F F, Lawless C, Hubbard S J, Fan J, Bessant C, Hermjakob H, Jones A R. A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS. 2012; 16 (9):431-42.
[15] Carvalho P C, Han X, Xu T, Cociorva D, da Gloria Carvalho M, Barbosa V C, et al. XDIA: Improving on the label-free data-independent analysis. Bioinformatics. 2010; 26 (6):847–848.
[16] Carvalho P C, Xu T, Han X, Cociorva D, Barbosa V C, Yates J R. YADA: A tool for taking the most out of high-resolution spectra. Bioinformatics. 2009; 25 (20):2734–2736.
[17] Pandeswari P B, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv. 2019; 9:313–44.
[18] Kumar D, Yadav A K, Dash D. (2017). Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data. In: Keerthikumar, S., Mathivanan, S. (eds) Proteome Bioinformatics. Methods in Molecular Biology, vol 1549. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6740-7_3
[19] Pandeswari P B, Sabareesh V. An ESI Q-TOF study to understand the impact of arginine on CID MS/MS characteristics of polypeptides. International Journal of Mass Spectrometry 2021, 459:116453.
[20] Patthy L, Smith E L. Reversible Modification of Arginine Residues. J. Biol. Chem. 1975; 250:557-564.
[21] Takahashi K. The Reaction of phenylglyoxal with arginine residues in proteins. J. Biol. Chem. 1968, 243:6171-6179.