libpappsomspp
Library for mass spectrometry
filtertandemremovec13.h
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1 /**
2  * \file pappsomspp/filers/filtertandemremovec13.h
3  * \date 26/04/2019
4  * \author Olivier Langella
5  * \brief new implementation of the X!Tandem filter to remove isotopes in an MS2
6  * signal
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  ******************************************************************************/
28 
29 #pragma once
30 
31 #include "filterinterface.h"
32 #include <cstddef>
33 
34 namespace pappso
35 {
36 
37 
38 /** @brief Deisotope the mass spectrum
39  * \c this mass spectrum is iterated over and according to a data point-based
40  * moving window progression does the following tests:
41  *
42  * - any data point having a x value (m/z value) less than 200 is conserved;
43  *
44  * - any data point having a x value greater than the previous data point's x
45  * value by at least 0.95 is conserved;
46  *
47  *
48 remove isotopes as in X!Tandem algorithm this method doesn't
49  * really remove isotopes: it cleans up multiple intensities within one
50  * Dalton of each other.
51 
52 
53  first tandem filter is 0.95 (remove_isotopes(_s);)
54  second tandem filter is 1.5 (clean_isotopes(_s);)
55  * */
56 
58 {
59 
60  public:
61  FilterTandemDeisotope(double mz_range_max = 0.95, double minimum_mz = 200.0);
63  MassSpectrum &filter(MassSpectrum &data_points) const override;
64 
65 
66  private:
67  double m_arbitrary_range_between_isotopes = 0.95;
68  double m_arbitrary_minimum_mz = 200.0;
69 };
70 } // namespace pappso
Deisotope the mass spectrum this mass spectrum is iterated over and according to a data point-based m...
generic interface to apply a filter on a MassSpectrum This is the same as FilterInterface,...
Class to represent a mass spectrum.
Definition: massspectrum.h:71
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39