ProForma Compliance

ProForma Parser Implementation Checklist

[x] Amino acids (+UO) - AAHCFKUOT (§6.1)
[x] Unimod names - PEM[Oxidation]AT (§6.2.1)
[x] PSI-MOD names - PEM[monohydroxylated residue]AT (§6.2.1)
[x] Unimod numbers - PEM[UNIMOD:35]AT (§6.2.2)
[x] PSI-MOD numbers - PEM[MOD:00425]AT (§6.2.2)
[x] Delta masses - PEM[+15.995]AT (§6.2.3)
[x] N-terminal modifications - [Carbamyl]-QPEPTIDE (§6.3)
[x] C-terminal modifications - PEPTIDEG-[Methyl] (§6.3)
[x] Labile modifications - {Glycan:Hex}EM[U:Oxidation]EV (§6.4)
[x] Multiple modifications - MPGNW[Oxidation][Carboxymethyl]PESQE (§6.5)
[x] Information tag - ELV[INFO:AnyString]IS (§6.6)

[x] Ambiguous amino acids - BZJX (§7.1)
[x] Prefixed delta masses - PEM[U:+15.995]AT (§7.2)
[x] Mass gap - PEX[+147.035]AT (§7.3)
[x] Formulas - PEM[Formula:O]AT, PEM[Formula:[17O1]]AT (§7.4)
[x] Mass with interpretation - PEM[+15.995|Oxidation]AT (§7.5)
[x] Unknown mod position - [Oxidation]?PEMAT (§7.6.1)
[x] Set of positions - PEP[Oxidation#1]M[#1]AT (§7.6.2)
[x] Range of positions - PRT(ESFRMS)[+19.0523]ISK (§7.6.3)
[x] Position scores - PEP[Oxidation#1(0.95)]M[#1(0.05)]AT (§7.6.4)
[x] Range position scores - (PEP)[Oxidation#1(0.95)]M[#1(0.05)]AT (§7.6.5)
[x] Amino acid ambiguity - (?VCH)AT (§7.7)
[x] Modification prefixes - PEPM[U:Oxidation]AS[M:O-phospho-L-serine] (§7.8)

[x] RESID modifications - EM[R:L-methionine sulfone]EM[RESID:AA0581] (§8.1)
[x] Names - (>Heavy chain)EVQLVESG (§8.2)

[x] XL-MOD modifications - EVTK[X:Aryl azide]LEK[XLMOD:00114]SEFD (§9.1)
[ ] Cross-linkers (intrachain) - EVTK[X:Aryl azide#XL1]LEK[#XL1]SEFD (§9.2.1)
[ ] Cross-linkers (interchain) - EVTK[X:Aryl azide#XL1]L//EK[#XL1]SEFD (§9.2.2)
[ ] Branches - ED[MOD:00093#BRANCH]//D[#BRANCH]ATR (§9.3)

[x] Charged formulas - SEQUEN[Formula:Zn1:z+2]CE (§11.1)
[x] Controlling placement - PTI(MERMERME)[+32|Position:E]PTIDE (§11.2)
[x] Global isotope - <13C>CARBON (§11.3.1)
[x] Fixed modifications - <[Oxidation]@M>ATPEMILTCMGCLK (§11.3.2)
[x] Chimeric spectra - NEEYN+SEQUEN (§11.4)
[x] Charges - SEQUEN/2, SEQUEN/[Na:z+1,H:z+1] (§11.5)
[x] Ion notation - SEQUEN-[b-type-ion] (§11.6)