ProteoWizard
MS2NoiseFilter.hpp
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1//
2// $Id: SpectrumList_PeakFilter.hpp 1191 2009-08-14 19:33:05Z chambm $
3//
4//
5// Original author: Chris Paulse <cpaulse <a.t> systemsbiology.org>
6//
7// Copyright 2009 Institute for Systems Biology, Seattle, WA
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#ifndef _MS2_NOISE_FILTER_HPP_
24#define _MS2_NOISE_FILTER_HPP_
25
26
30
31
32namespace pwiz {
33namespace analysis {
34
35
36// Noise peak removal in ms2 spectra. We expect fragment masses to be relatively
37// equally spaced throughout the spectrum. Select the top n most intense ions within a
38// sliding window width of w. Optionally, allow more peaks at lower mass (below precursor).
39//
40// Reference:
41// "When less can yield more – Computational preprocessing of MS/MS spectra for peptide
42// identification", Bernhard Y. Renard, Marc Kirchner␂, Flavio Monigatti␂, Alexander R. Ivanov,
43// Juri Rappsilber, Dominic Winter, Judith A. J. Steen, Fred A. Hamprecht and Hanno Steen
44// Proteomics, 9, 4978-4984, 2009.
45
47{
48 /// MS2NoiseFilter's parameters
50 {
52 int numMassesInWindow_ = 5,
53 double windowWidth_ = 120.0,
54 bool relaxLowMass_ = false
55 );
56
60 };
61
62 MS2NoiseFilter(const MS2NoiseFilter::Config params_) : params(params_) {}
63 virtual void operator () (const pwiz::msdata::SpectrumPtr&) const;
65
67};
68
69
70} // namespace analysis
71} // namespace pwiz
72
73
74#endif // _MS2_NOISE_FILTER_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
boost::shared_ptr< Spectrum > SpectrumPtr
Definition MSData.hpp:573
Config(int numMassesInWindow_=5, double windowWidth_=120.0, bool relaxLowMass_=false)
const MS2NoiseFilter::Config params
MS2NoiseFilter(const MS2NoiseFilter::Config params_)
virtual void describe(pwiz::msdata::ProcessingMethod &) const
Description of the default peak processing method. This element describes the base method used in the...
Definition MSData.hpp:255