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/**
* \file test/test_proforma.cpp
* \date 21/01/2025
* \author Olivier Langella
* \brief test proforma notation
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
// ./tests/catch2-only-tests [proforma] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <pappsomspp/core/peptide/peptideproformaparser.h>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
#include "common.h"
#include "tests/tests-config.h"
/// home/langella/developpement/git/i2masschroq/src/input/sage/sagetsvhandler.cpp@457,
/// SageTsvHandler::parsePeptide(): "[+42.0106]-M[MOD:00719]QNDAGEFVDLYVPR"
// https://pmc.ncbi.nlm.nih.gov/articles/PMC7612572/
// https://github.com/HUPO-PSI/ProForma/blob/master/SpecDocument/ProForma_v2_draft15_February2022.pdf
TEST_CASE("Test proforma notation", "[proforma]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Test ProForma parser ::..", "[proforma]")
{
REQUIRE_THROWS_AS(
PeptideProFormaParser::parseString("C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[FAVEGPK"),
pappso::ExceptionNotPossible);
qDebug();
PeptideSp peptide_from_str = PeptideProFormaParser::parseString(
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAVEGPK");
REQUIRE(peptide_from_str.get()->getMass() == Catch::Approx(1909.764470427));
REQUIRE(peptide_from_str.get()->toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAVEGPK");
PeptideSp peptide_from_str2 = PeptideProFormaParser::parseString(
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDK[-18.02]EAC[MOD:00397]FAVEGPK");
/*REQUIRE(peptide_from_str2.get()->toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDK[-18.0200]EAC[MOD:00397]"
"FAVEGPK");*/
REQUIRE(peptide_from_str2.get()->getMass() == Catch::Approx(1891.744470427));
REQUIRE(peptide_from_str2.get()->toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDK[MOD:00704]EAC[MOD:00397]FAVEGPK");
PeptideSp peptide_nter_modif_acetyl =
PeptideProFormaParser::parseString("M[MOD:00408][MOD:00719]QNDAGEFVDLYVPR");
REQUIRE(peptide_nter_modif_acetyl.get()->getMass() == Catch::Approx(1810.8195998027));
PeptideSp peptide_nter_modif =
PeptideProFormaParser::parseString("[+42.0106]-M[MOD:00719]QNDAGEFVDLYVPR");
REQUIRE(peptide_nter_modif.get()->getMass() == Catch::Approx(1810.8195998027));
REQUIRE(peptide_nter_modif.get()->toProForma().toStdString() ==
"[MOD:00408]-M[MOD:00719]QNDAGEFVDLYVPR");
PeptideSp peptide_nter_modif_acetylstr =
PeptideProFormaParser::parseString("[Acetyl]-M[MOD:00719]QNDAGEFVDLYVPR");
REQUIRE(peptide_nter_modif_acetylstr.get()->getMass() == Catch::Approx(1810.8195998027));
REQUIRE(peptide_nter_modif_acetylstr.get()->toProForma().toStdString() ==
"[UNIMOD:1]-M[MOD:00719]QNDAGEFVDLYVPR");
PeptideSp peptide_nter_modif_acetylstr2 =
PeptideProFormaParser::parseString("M[Acetyl][MOD:00719]QNDAGEFVDLYVPR");
PeptideSp peptide_nter_modif_acetylstr3 =
PeptideProFormaParser::parseString("[Acetyl]-M[MOD:00719]QNDAGEFVDLYVPR");
REQUIRE(peptide_nter_modif_acetylstr2.get()->getMass() == Catch::Approx(1810.8195998027));
REQUIRE_FALSE(*peptide_nter_modif_acetylstr2.get() == *peptide_nter_modif_acetylstr.get());
REQUIRE(*peptide_nter_modif_acetylstr3.get() == *peptide_nter_modif_acetylstr.get());
// EM[Oxidation]EVEES[Phospho]PEK
peptide_from_str = PeptideProFormaParser::parseString("EM[Oxidation]EVEES[Phospho]PEK");
REQUIRE(peptide_from_str.get()->getMass() == Catch::Approx(1301.4734300238));
REQUIRE(peptide_from_str.get()->toProForma().toStdString() ==
"EM[UNIMOD:35]EVEES[UNIMOD:21]PEK");
// EM[MOD:00719]EVEES[MOD:00046]PEK
peptide_from_str = PeptideProFormaParser::parseString("EM[MOD:00719]EVEES[MOD:00046]PEK");
REQUIRE(peptide_from_str.get()->getMass() == Catch::Approx(1301.4734300238));
REQUIRE(peptide_from_str.get()->toProForma().toStdString() ==
"EM[MOD:00719]EVEES[MOD:00046]PEK");
// SEQUEN[Formula:C12H20O2]CE
//[iTRAQ4plex]-EMEVNESPEK
peptide_from_str = PeptideProFormaParser::parseString("[iTRAQ4plex]-EMEVNESPEK");
REQUIRE(peptide_from_str.get()->getMass() == Catch::Approx(1334.6145817573));
REQUIRE(peptide_from_str.get()->toProForma().toStdString() == "[UNIMOD:214]-EMEVNESPEK");
// ELVIS[Phospho|INFO:newly discovered]K
//[-48.0042]?F[+189.1164]INIVER
peptide_from_str = PeptideProFormaParser::parseString("[-48.0042]?F[+189.1164]INIVER");
REQUIRE(peptide_from_str.get()->getMass() == Catch::Approx(1078.6185520281));
REQUIRE(peptide_from_str.get()->toProForma().toStdString() == "F[+189.1164]INIVER");
}
SECTION("..:: Test ProForma parser C13 N15 ::..", "[proforma]")
{
/*
4.6.1 Use Case 1: Representation of isotopes
This might be used in the case of synthetic peptides with 100% incorporation.
Example: Consider extension for 13C on all residues:
Carbon 13: <13C>ATPEILTVNSIGQLK
Nitrogen 15: <15N>ATPEILTVNSIGQLK
Deuterium: <D>ATPEILTVNSIGQLK
The representation of multiple isotopes is also possible. They can be located in any order.
Both Carbon 13 and Nitrogen 15: <13C><15N>ATPEILTVNSIGQLK
Distributions of isotope masses could be supported in future work.
4.6.2 Use Case 2: Fixed protein modifications
This mechanism can be useful especially in the case of full proteoforms. The affected
amino acid MUST be indicated using @. If more than one residue were affected, they
MUST be comma separated. Examples:
<[S-carboxamidomethyl-L-cysteine]@C>ATPEILTCNSIGCLK
<[MOD:01090]@C>ATPEILTCNSIGCLK
<[Oxidation]@C,M>MTPEILTCNSIGCLK
Fixed modifications MUST be written prior to ambiguous and labile modifications, and
similar to ambiguity notation, N-terminal modifications MUST be the last ones written,
just next to the sequence.
ProForma 2.0 (Proteoform and Peptidoform Notation) February 3, 2022
21
http://psidev.info/proforma
The following examples would be valid:
<[MOD:01090]@C>[Phospho]?EM[Oxidation]EVTSECSPEK
<[MOD:01090]@C>[Acetyl]-EM[Oxidation]EVTSECSPEK
*/
PeptideSp peptide_C13 = PeptideProFormaParser::parseString("<13C>ATPEILTVNSIGQLK");
REQUIRE(peptide_C13.get()->toProForma().toStdString() == "<13C>ATPEILTVNSIGQLK");
REQUIRE(peptide_C13.get()->getChemicalFormula().toString().toStdString() ==
"(13)C 70 H 122 N 18 O 23");
REQUIRE(peptide_C13.get()->getChemicalFormula().getMass() == Catch::Approx(1653.1278609157));
PeptideSp peptide_C13N15 = PeptideProFormaParser::parseString("<13C><15N>ATPEILTVNSIGQLK");
REQUIRE(peptide_C13N15.get()->toProForma().toStdString() == "<13C><15N>ATPEILTVNSIGQLK");
REQUIRE(peptide_C13N15.get()->getChemicalFormula().getMass() == Catch::Approx(1671.0744889969));
REQUIRE(peptide_C13N15.get()->getChemicalFormula().toString().toStdString() ==
"(13)C 70 (15)N 18 H 122 O 23");
PeptideSp peptide_carba =
PeptideProFormaParser::parseString("<[MOD:01090]@C>[Acetyl]-EM[Oxidation]EVTSECSPEK");
REQUIRE(peptide_carba.get()->toProForma().toStdString() ==
"[UNIMOD:1]-EM[UNIMOD:35]EVTSEC[MOD:01090]SPEK");
}
SECTION("..:: Test ProForma parser fixed modifications ::..", "[proforma]")
{
//<[S-carboxamidomethyl-L-cysteine]@C>ATPEILTCNSIGCLK
//<[MOD:01090]@C>ATPEILTCNSIGCLK
//<[Oxidation]@C,M>MTPEILTCNSIGCLK
PeptideSp peptide_carba =
PeptideProFormaParser::parseString("<[Oxidation]@C,M>MTPEILTCNSIGCLK");
REQUIRE(peptide_carba.get()->toProForma().toStdString() ==
"M[UNIMOD:35]TPEILTC[UNIMOD:35]NSIGC[UNIMOD:35]LK");
peptide_carba = PeptideProFormaParser::parseString("<[MOD:01090]@C>ATPEILTCNSIGCLK");
REQUIRE(peptide_carba.get()->toProForma().toStdString() ==
"ATPEILTC[MOD:01090]NSIGC[MOD:01090]LK");
/*
peptide_carba =
PeptideProFormaParser::parseString("<[S-carboxamidomethyl-L-cysteine]@C>ATPEILTCNSIGCLK");
REQUIRE(peptide_carba.get()->toProForma().toStdString() ==
"[UNIMOD:1]-EM[UNIMOD:35]EVTSECSPEK");
*/
}
SECTION("..:: Test ProForma parser Nter Cter ::..", "[proforma]")
{
//[iTRAQ4plex]-EM[U:Oxidation]EVNES[Phospho]PEK[iTRAQ4plex]-[Methyl]
PeptideSp peptide =
PeptideProFormaParser::parseString("[iTRAQ4plex]-EM[Oxidation]EVNES[Phospho]PEK[iTRAQ4plex]");
PeptideSp peptide_cter = PeptideProFormaParser::parseString(
"[iTRAQ4plex]-EM[Oxidation]EVNES[Phospho]PEK[iTRAQ4plex]-[Methyl]");
REQUIRE(peptide_cter.get()->toProForma().toStdString() ==
"[UNIMOD:214]-EM[UNIMOD:35]EVNES[UNIMOD:21]PEK[UNIMOD:214]-[UNIMOD:34]");
REQUIRE(peptide_cter.get()->toAbsoluteString().toStdString() ==
"E(internal:Nter_hydrolytic_cleavage_H,UNIMOD:214)M(UNIMOD:35)EVNES(UNIMOD:21)PEK("
"internal:Cter_hydrolytic_cleavage_HO,UNIMOD:34,UNIMOD:214)");
// xref: delta_mono_mass "14.01565"
REQUIRE((peptide_cter.get()->getMass() - peptide.get()->getMass()) ==
Catch::Approx(14.0156500645));
pappso::ChemicalFormula formula = peptide.get()->getChemicalFormula();
pappso::ChemicalFormula formula_cter = peptide_cter.get()->getChemicalFormula();
formula = formula_cter + -formula;
REQUIRE(formula.toString().toStdString() == "C 1 H 2");
REQUIRE(formula.getMass() == Catch::Approx(14.0156500645));
formula = peptide.get()->getChemicalFormula() + -peptide_cter.get()->getChemicalFormula();
REQUIRE(formula.toString().toStdString() == "C -1 H -2");
REQUIRE(formula.getMass() == Catch::Approx(-14.0156500645));
}
}
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