Two sequences are used to demonstrate the structure of our processed information file. The text line after the “>” symbol contains accession numbers associated with the sequence. The other rows each contains six entries separated by tabs. The first column indicates the residue position. The second column indicates the modified residue(s) that can occur at the position specified in the first column. The third column, labeled by either SAP or PTM, indicates the modification type. The fifth column contains the accession number of the source of modification, this may be a protein sequence or mRNA. When the source of modification is obtained from proteotypic consensus peptide within a spectral library, the fifth column shows the proteotypic peptide instead. The fourth column explains the nature of the modification; a lower case letter indicates residue content in the source sequence, the upper case letter indicates the modified residue in the variant sequence. The notation, v → I, indicates the source sequence with amino acid V can change into I, ie, a SAP. The notation, gT C → A, is a short hand for codon change from gtc to atc, ie, a SNP that changes the coded amino acid from V to I as well. The sixth column contains additional information for the fourth column. It may include disease information, database entry index, or spectral indices when the modification is associated with a proteotypic peptide. As an example, the post-translational modification (M06) at position 59 of the second sequence is observed in the following proteotypic peptides: PDETM06VIGNYR, CFIEEIPDETM06VIGNYR, FHIGETEKKC-FIEEIPDETM06VIGNYR and CFIEEIPDETM06VIGNYR. The first three are obtained from spectra of GPM (human_cmp_20) spectral library with spectral indices 134010, 442918, 442918, 442920, and 589710, while the fourth one came from the NIST (#NIST_human_IT_v3.0) spectral library with spectral indices 25094 and 25102.
