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We found no evidence of tenascin C fragmentation in Matn3 V194D and Comp DelD469 samples since the examination of matched peptides did not reveal any genotype specific differences in sequence coverage (data not shown).
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NMP, the number of matched peptides.
f No. MP: number of matched peptides.
hPercentage of predicted protein sequence covered by matched peptides.
Based on the Mascot search results, 9660 spectra matched known spectra, 9177 spectra matched unique peptides, 3880 matched peptides, 3757 matched unique peptides, and 1282 matched proteins (Additional file 1: Figure S2 (A), Additional file 2: Table S1), respectively.
Upon closer inspection, 35 of the 76 peptides did not match isoform 2, but all 76 of the peptides were found to match alpha-1-antichymotrypsin isoform 1 instead (IPI00550991).
f Number of matched peptide masses.
Due to the small number of observed mismatched modification positions among the overlaps between SIMS and MODmap (14 of 119 matching peptide sequences (∼12%)), we did not observe any improvement post-processed with PTMClust.
Although searches to find ST genes retrieve many low-similarity sequences in most genomes, several matches do not have an associated ORF or the peptides do not show ST characteristics, as described below.
These peptides do not undergo self-assembly.
those where the cluster did not include a "best" filtered model but still contained models with matching peptide identifications, and c).
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