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Fill the four N-terminal probe adducts #459

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8 changes: 4 additions & 4 deletions alphabase/constants/const_files/modification.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2936,8 +2936,8 @@ CP-DTB@W 0.0 0.0 C(27)H(44)N(10)O(7) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(C
CP-DTB-heavy@W 0.0 0.0 13C(4)15N(2)C(23)H(44)N(8)O(7) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CC(=C(N(C)C(=O)OCCCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)N2)C1=C2C=CC=C1)C(=O)[Ts] 0.0
EBA-DTB@K 0.0 0.0 C(32)H(41)N(9)O(6) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CCCC[n+]%12ccc%13ccc(OCc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cc%13c%12)C(=O)[Ts] 0.0
EBA-DTB-heavy@K 0.0 0.0 13C(4)15N(2)C(28)H(41)N(7)O(6) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CCCC[n+]%12ccc%13ccc(OCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cc%13c%12)C(=O)[Ts] 0.0
EBA-DTB@Any_N-term 0.0 0.0 C(32)H(41)N(9)O(6) 0.0 User-added 0 0.0
EBA-DTB-heavy@Any_N-term 0.0 0.0 13C(4)15N(2)C(28)H(41)N(7)O(6) 0.0 User-added 0 0.0
EBA-DTB@Any_N-term 0.0 0.0 C(32)H(41)N(9)O(6) 0.0 User-added 0 [Lv+]%12C=CC%13=CC=C(OCc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)C=C%13C=%12 0.0

@lucas-diedrich lucas-diedrich Oct 16, 2026

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Current molecule

Image

Checks

Structure matches the product of the reaction mechanism in this publication:

Image

Issues

Stereoconformation at the 4-Methylimidazolidin-2-one ring seems to be different than in this structure of a vendor (see arrangement of methyl/alkyl groups at the two chiral centers)

Not saying that the vendor structure is correct though ...

Image

EBA-DTB-heavy@Any_N-term 0.0 0.0 13C(4)15N(2)C(28)H(41)N(7)O(6) 0.0 User-added 0 [Lv+]%12C=CC%13=CC=C(OCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)C=C%13C=%12 0.0
Comment thread
lucas-diedrich marked this conversation as resolved.
Resolved
EBX1-DTB@C 0.0 0.0 C(27)H(41)N(9)O(6) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CSC#CCCOCc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)C(=O)[Ts] 0.0
EBX1-DTB-heavy@C 0.0 0.0 13C(4)15N(2)C(23)H(41)N(7)O(6) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CSC#CCCOCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)C(=O)[Ts] 0.0
EBX2-DTB@C 0.0 0.0 C(22)H(35)N(9)O(5) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CSc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)C(=O)[Ts] 0.0
Expand Down Expand Up @@ -3092,8 +3092,8 @@ OxMet2-DTB@M 0.0 0.0 C(29)H(47)N(11)O(7) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H
OxMet2-DTB-heavy@M 0.0 0.0 13C(4)15N(2)C(25)H(47)N(9)O(7) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CCS(C)=NC(=O)N%12CCC(OCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)CC%12)C(=O)[Ts] 0.0
PCA-DTB@K 0.0 0.0 C(28)H(38)N(10)O(5) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CCCCN=Cc%12ccc(c%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cn%12)C(=O)[Ts] 0.0
PCA-DTB-heavy@K 0.0 0.0 13C(4)15N(2)C(24)H(38)N(8)O(5) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CCCCN=Cc%12ccc(c%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cn%12)C(=O)[Ts] 0.0
PCA-DTB@Any_N-term 0.0 0.0 C(28)H(38)N(10)O(5) 0.0 User-added 0 0.0
PCA-DTB-heavy@Any_N-term 0.0 0.0 13C(4)15N(2)C(24)H(38)N(8)O(5) 0.0 User-added 0 0.0
PCA-DTB@Any_N-term 0.0 0.0 C(28)H(38)N(10)O(5) 0.0 User-added 0 [Lv]=Cc%12ccc(c%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cn%12 0.0

@lucas-diedrich lucas-diedrich Oct 16, 2026

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Current molecule

Image

Checks

  • Same comment with respect to the stereochemistry of the two chiral centers as for EBA-DTB@Any_N-term
  • The current smiles string encodes the initial product, a Schiff Base, which will (according to claude) rearrange during sample processing:

(Claude)
Image

PCA-DTB-heavy@Any_N-term 0.0 0.0 13C(4)15N(2)C(24)H(38)N(8)O(5) 0.0 User-added 0 [Lv]=Cc%12ccc(c%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)cn%12 0.0
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Resolved
PFPSA-DTB@C 0.0 0.0 C(30)H(40)N(10)O(7)S(1)F(4) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CSc%12c(F)c(F)c(S(=O)(=O)NCCc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)c(F)c%12F)C(=O)[Ts] 0.0
PFPSA-DTB-heavy@C 0.0 0.0 13C(4)15N(2)C(26)H(40)N(8)O(7)F(4)S(1) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CSc%12c(F)c(F)c(S(=O)(=O)NCCc%11cn(CCCC[C@@H](C(N)=O)N[13C](=O)[13CH2][15NH][13C](=O)[13CH2][15NH]C(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)c(F)c%12F)C(=O)[Ts] 0.0
PFPSA-DTB@H 0.0 0.0 C(30)H(40)N(10)O(7)S(1)F(4) 0.0 User-added 0 N([Fl])([Fl])[C@@]([H])(CC1=CN(c%12c(F)c(F)c(S(=O)(=O)NCCc%11cn(CCCC[C@@H](C(N)=O)NC(=O)CNC(=O)CNC(=O)CCCCC[C@H]%10NC(=O)N[C@@H]%10C)nn%11)c(F)c%12F)C=N1)C(=O)[Ts] 0.0
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