Fig. 1. Overview of the entire method for aggregated strings generation. (a) Extraction of 3-tags from the input set of deconvoluted MS/MS spectra. (b)

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Fig. 1. Overview of the entire method for aggregated strings generation. (a) Extraction of 3-tags from the input set of deconvoluted MS/MS spectra. (b) Assembly of a de novo string from five 3-tags consistent with each other in terms of both amino acid sequences and offsets. The resulting de novo string ‘DSTVYN’ is assigned the mass offset of 100 with multiplicity 5. (c) Formation of an aggregated string from three de novo string endowed with offsets. The resulting aggregated string ‘DSTVYNP’ has the main direct and reversed offset of 100 and 124, respectively, which leads to the precursor mass estimate PM DSTVYNP=100+Mass(DSTVYNP)+124=1000 From: Top-down analysis of protein samples by de novo sequencing techniques Bioinformatics. 2016;32(18):2753-2759. doi:10.1093/bioinformatics/btw307 Bioinformatics | © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Fig. 2. Overview of the procedure generating the set of aggregated strings from a set of de novo amino acid strings obtained using the Twister approach (Vyatkina et al., 2015) From: Top-down analysis of protein samples by de novo sequencing techniques Bioinformatics. 2016;32(18):2753-2759. doi:10.1093/bioinformatics/btw307 Bioinformatics | © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Fig. 3. (a–c) Processing the alemtuzumab dataset: handling the 4-mer ‘GTQL’ with the score 8. (a) The set of active strings containing ‘GTQL’ or ‘LQTG’. (b) The aligned strings (duplications due to string reversal are not shown). (c) Clusterization: the string ‘VGTQLNEMTQS’ did not match well the main string ‘PVGTQLNNTNYLLL’, and gave rise to the second cluster; each of the strings ‘GTQLS’ and ‘GTQLD’ produced one mismatch when being aligned against ‘PVGTQLNNTNYLLL’ or ‘VGTQLNEMTQS’, and thus, both were placed in the third cluster. (d) The aggregated string with the amino acid sequence ‘PVGTQLNNTNYLLL’ (at the bottom) was obtained at time of processing the 4-mer ‘VGTQ’ with the score 25. The first four amino acids of its underlying consensus string ‘SDLSPVGTQLNNTNYLLL’ were eliminated by the validation procedure. Incorrect candidate amino acids in the aligned strings are marked gray (the amino acid scores are not shown). A 4-mer being processed and its reversed copy are highlighted From: Top-down analysis of protein samples by de novo sequencing techniques Bioinformatics. 2016;32(18):2753-2759. doi:10.1093/bioinformatics/btw307 Bioinformatics | © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com