Table 2.
Examples of ProForma 2.0 notations demonstrating the various features of the specification. For each feature listed in the first column, there is a representative example in the second column showing the encoding. The “Section” column provides the location in the PSI specification document where the feature is explained in detail (Supplementary Document 1).
| Feature | Example | Section |
|---|---|---|
| CV/ontology modification names | EM[Oxidation]EVEES[Phospho]PEK | 4.2.1 |
| CV/ontology protein modification accession numbers | EM[MOD:00719]EVEES[MOD:00046]PEK | 4.2.2 |
| Cross-link within the same peptide | EMEVTK[XLMOD:02001#XL1]SESPEK[#XL1] | 4.2.3.1 |
| Inter-chain cross-links | SEK[XLMOD:02001#XL1]UENCE//EMEVTK[#XL1]SESPEK | 4.2.3.2 |
| Disulfide linkages | EVTSEKC[MOD:00034#XL1]LEMSC[#XL1]EFD | 4.2.3.3 |
| Branched peptides | ETFGD[MOD:00093#BRANCH]//R[#BRANCH]ATER | 4.2.4 |
| Glycans using the GNO ontology as CV | NEEYN[GNO:G59626AS]K | 4.2.5 |
| Delta mass notation for modifications | EM[+15.9949]EVEES[+79.9663]PEK | 4.2.6 |
| Specifying a gap of known mass | RTAAX[+367.0537]WT | 4.2.7 |
| Support for elemental formulas | SEQUEN[Formula:C12H20O2]CE | 4.2.8 |
| Glycan composition | SEQUEN[Glycan:HexNAc1Hex2]CE | 4.2.9 |
| N-terminal and C-terminal modifications | [iTRAQ4plex]-EMEVNESPEK | 4.3.1 |
| Labile modifications | {Glycan:Hex}EMEVNESPEK | 4.3.2 |
| Unknown modification position | [Phospho]?EMEVTSESPEK | 4.4.1 |
| Possible set of modification positions | EMEVT[#g1]S[#g1]ES[Phospho#g1]PEK | 4.4.2 |
| Ranges of positions for the modifications | PROT(ESFRMS)[+19.0523]ISK | 4.4.3 |
| Modification position preference and localization scores | EMEVT[#g1(0.01)]S[#g1(0.09)]ES[Phospho#g1(0.90)]PEK | 4.4.4 |
| Scoring for ranges of positions for a modification | PROT(ESFRMS)[+19.0523#g1(0.01)]ISK[#g1(0.99)] | 4.4.5 |
| Isotopes | <13C>ATPEILTVNSIGQLK | 4.6.1 |
| Fixed protein modifications | <[MOD:01090]@C>ATPEILTCNSIGCLK | 4.6.2 |
| Ambiguity in the order of the amino acid sequence | (?DQ)NGTWEMESNENFEGYMK | 4.7 |
| Information tag | ELVIS[Phospho|INFO:newly discovered]K | 4.8 |
| Joint representation of experimental data and interpretation | ELVIS[Phospho|Obs:+79.978]K | 4.9 |
| Representation of ion charges | EMEVEESPEK/2 | 7.1 |
| Multiple peptidoforms assigned to chimeric spectra | EMEVEESPEK/2+ELVISLIVER/3 | 7.1 |