From a58f06b8f1992f9088b5450c63010a347fd3ab6b Mon Sep 17 00:00:00 2001 From: WassimG Date: Thu, 7 Nov 2024 15:19:08 +0000 Subject: [PATCH] fix var mods for maxquant to work with the ptm model --- spectrum_fundamentals/constants.py | 43 +++++++++++++++--------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/spectrum_fundamentals/constants.py b/spectrum_fundamentals/constants.py index 8f48484..1e68d9a 100644 --- a/spectrum_fundamentals/constants.py +++ b/spectrum_fundamentals/constants.py @@ -80,27 +80,28 @@ ###################### MAXQUANT_VAR_MODS = { - "(ox)": "[UNIMOD:35]", - "(Oxidation (M))": "[UNIMOD:35]", - "(tm)": "[UNIMOD:737]", - "_(tm)": "_[UNIMOD:737]-", - "K(tm)": "K[UNIMOD:737]", - "(i4)": "[UNIMOD:214]", - "_(i4)": "_[UNIMOD:214]-", - "K(i4)": "K[UNIMOD:214]", - "(i8)": "[UNIMOD:730]", - "_(i8)": "_[UNIMOD:730]-", - "K(i8)": "K[UNIMOD:730]", - "(tmp)": "[UNIMOD:2016]", - "_(tmp)": "_[UNIMOD:2016]-", - "K(tmp)": "K[UNIMOD:2016]", - "(ph)": "[UNIMOD:21]", - "(Phospho (STY))": "[UNIMOD:21]", - "(de)": "[UNIMOD:23]", - "(Dehydrated (ST))": "[UNIMOD:23]", - "K(Lys8)": "K[UNIMOD:259]", - "R(Arg10)": "R[UNIMOD:267]", - "C(Carbamidomethyl (C))": "C[UNIMOD:4]", + "\\(ox\\)": "[UNIMOD:35]", + "\\(Oxidation\\ \\(M\\)\\)": "[UNIMOD:35]", + "\\(tm\\)": "[UNIMOD:737]", + "_\\(tm\\)": "_[UNIMOD:737]-", + "K\\(tm\\)": "K[UNIMOD:737]", + "\\(i4\\)": "[UNIMOD:214]", + "_\\(i4\\)": "_[UNIMOD:214]-", + "K\\(i4\\)": "K[UNIMOD:214]", + "\\(i8\\)": "[UNIMOD:730]", + "_\\(i8\\)": "_[UNIMOD:730]-", + "K\\(i8\\)": "K[UNIMOD:730]", + "\\(tmp\\)": "[UNIMOD:2016]", + "_\\(tmp\\)": "_[UNIMOD:2016]-", + "K\\(tmp\\)": "K[UNIMOD:2016]", + "\\(ph\\)": "[UNIMOD:21]", + "\\(Phospho\\ \\(STY\\)\\)": "[UNIMOD:21]", + "\\(de\\)": "[UNIMOD:23]", + "\\(Dehydrated \\(ST\\)\\)": "[UNIMOD:23]", + "K\\(Lys8\\)": "K[UNIMOD:259]", + "R\\(Arg10\\)": "R[UNIMOD:267]", + "C\\(Carbamidomethyl\\ \\(C\\)\\)": "C[UNIMOD:4]", + "C": "C[UNIMOD:4]", } MAXQUANT_NC_TERM = {"^_": "", "_$": ""}