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Expand elastase|P cleavage specificity #1100

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Expand elastase|P cleavage specificity #1100

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2 changes: 1 addition & 1 deletion mzLib/Proteomics/ProteolyticDigestion/proteases.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ Arg-C R| full MS:1001303 Arg-C
Asp-N |D full MS:1001304 Asp-N
chymotrypsin|P F[P]|,W[P]|,Y[P]|,L[P]| full MS:1001306 Chymotrypsin
CNBr M| full MS:1001307 CNBr Homoserine lactone on M
elastase|P A[P]|,V[P]|,S[P]|,G[P]|,L[P]|,I[P]| full Elastase
elastase|P I[P]|,S[P]|,L[P]|,V[P]|,N[P]|,T[P]|,K[P]|,A[P]|,G[P]|,Y[P]|,Q[P]|,R[P]|,F[P]|,D[P]| full Elastase
Glu-C E| full
Glu-C (with asp) E|,D| full
Lys-C|P K[P]| full MS:1001309 Lys-C
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6 changes: 4 additions & 2 deletions mzLib/Test/ProteomicsTests/ProteolyticDigestion/PeptideWithSetModsDecoyTests.cs
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Expand Up @@ -102,11 +102,13 @@ public static void TestReverseDecoyFromTarget()
Assert.AreEqual("MKEITPMEP", p_cnbr_reverse.BaseSequence);
Assert.AreEqual(p_cnbr.FullSequence, p_cnbr_reverse.PeptideDescription);

// elastase cleave after A, V, S, G, L, I,
// elastase cleave after I, S, L, V, N, T, K, A, G, Y, Q, R, F, D (not before P)
// Only V(3, blocked by the following P), P(4) and H(8) are not cleavage residues,
// so every other position is pinned and just those three are reversed into place.
newAminoAcidPositions = new int["KAYVPSRGHLDIN".Length];
PeptideWithSetModifications p_elastase = new PeptideWithSetModifications(new Protein("KAYVPSRGHLDIN", "DECOY_ELASTASE"), new DigestionParams(protease: "elastase|P"), 1, 13, CleavageSpecificity.Semi, null, 0, new Dictionary<int, Modification>(), 0, null);
PeptideWithSetModifications p_elastase_reverse = p_elastase.GetReverseDecoyFromTarget(newAminoAcidPositions);
Assert.AreEqual("NADHRSPGVLYIK", p_elastase_reverse.BaseSequence);
Assert.AreEqual("KAYHPSRGVLDIN", p_elastase_reverse.BaseSequence);

// top-down
newAminoAcidPositions = new int["RPEPTIREK".Length];
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