. Author manuscript; available in PMC: 2020 Jan 4.

Published in final edited form as: J Proteome Res. 2018 Oct 31;18(1):349–358. doi: 10.1021/acs.jproteome.8b00651

Table 1.

Common Sequence Similarity Types and Their Frequencies in Nonspliced and Cis-Spliced Searches

	Observed Peptide	Similar Sequence^a	Nonspliced Frequency^b	Cis-Spliced Frequency^b
Permutation	CQMMQNPRACLEMS	QCMMQNPRAGLEMS	1.42E-3	0.660
Replacement	CQMMQNPRACLEMS	CQMMQNPRAGLDMT	2.57E-4	0.384
Insertion	CQMMQNPRAGLEMS	CQMMQGGPRAGLEMS	2.56E-5	0.106
Deletion	CQMMQNPRAGLEMS	CQMMQN PRQLEMS	Ί.76Ε−5	0.054
Substitution	CQMMQNPRAGLEMS	CQMMQNPRAGLEME	1.69E-4	0.265
	Acetyl

These sequences have identical precursor masses and similar fragmentation patterns, making the correct sequence diffcult to distinguish.

Frequencies are the average number of similar sequences per theoretical peptide. This was calculated for 9-mer, nonspliced peptides from the human.xml database. The computational power required for this calculation limited the similarity comparisons to peptides generated from the same protein. The database-wide frequencies are thus expected to be much higher.