void IsobaricChannelExtractor::extractChannels(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map)
{
if (ms_exp_data.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.\n";
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Experiment has no scans!");
}
// clear the output map
consensus_map.clear(false);
consensus_map.setExperimentType("labeled_MS2");
// create predicate for spectrum checking
LOG_INFO << "Selecting scans with activation mode: " << (selected_activation_ == "" ? "any" : selected_activation_) << "\n";
HasActivationMethod<MSExperiment<Peak1D>::SpectrumType> activation_predicate(StringList::create(selected_activation_));
// now we have picked data
// --> assign peaks to channels
UInt64 element_index(0);
// remember the current precusor spectrum
MSExperiment<Peak1D>::ConstIterator prec_spec = ms_exp_data.end();
for (MSExperiment<Peak1D>::ConstIterator it = ms_exp_data.begin(); it != ms_exp_data.end(); ++it)
{
// remember the last MS1 spectra as we assume it to be the precursor spectrum
if (it->getMSLevel() == 1) prec_spec = it;
if (selected_activation_ == "" || activation_predicate(*it))
{
// check if precursor is available
if (it->getPrecursors().empty())
{
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, String("No precursor information given for scan native ID ") + it->getNativeID() + " with RT " + String(it->getRT()));
}
// check precursor constraints
if (!isValidPrecursor_(it->getPrecursors()[0]))
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor doesn't fulfill all constraints." << std::endl;
continue;
}
// check precursor purity if we have a valid precursor ..
if (prec_spec != ms_exp_data.end())
{
const DoubleReal purity = computePrecursorPurity_(it, prec_spec);
if (purity < min_precursor_purity_)
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor purity is below the threshold. [purity = " << purity << "]" << std::endl;
continue;
}
}
else
{
LOG_INFO << "No precursor available for spectrum: " << it->getNativeID() << std::endl;
}
if (!(prec_spec == ms_exp_data.end()) && computePrecursorPurity_(it, prec_spec) < min_precursor_purity_)
{
LOG_DEBUG << "Skip spectrum " << it->getNativeID() << ": Precursor purity is below the threshold." << std::endl;
continue;
}
// store RT&MZ of parent ion as centroid of ConsensusFeature
ConsensusFeature cf;
cf.setUniqueId();
cf.setRT(it->getRT());
cf.setMZ(it->getPrecursors()[0].getMZ());
Peak2D channel_value;
channel_value.setRT(it->getRT());
// for each each channel
UInt64 map_index = 0;
Peak2D::IntensityType overall_intensity = 0;
for (IsobaricQuantitationMethod::IsobaricChannelList::const_iterator cl_it = quant_method_->getChannelInformation().begin();
cl_it != quant_method_->getChannelInformation().end();
++cl_it)
{
// set mz-position of channel
channel_value.setMZ(cl_it->center);
// reset intensity
channel_value.setIntensity(0);
// as every evaluation requires time, we cache the MZEnd iterator
const MSExperiment<Peak1D>::SpectrumType::ConstIterator mz_end = it->MZEnd(cl_it->center + reporter_mass_shift_);
// add up all signals
for (MSExperiment<Peak1D>::SpectrumType::ConstIterator mz_it = it->MZBegin(cl_it->center - reporter_mass_shift_);
mz_it != mz_end;
++mz_it)
{
channel_value.setIntensity(channel_value.getIntensity() + mz_it->getIntensity());
}
// discard contribution of this channel as it is below the required intensity threshold
if (channel_value.getIntensity() < min_reporter_intensity_)
{
channel_value.setIntensity(0);
}
overall_intensity += channel_value.getIntensity();
// add channel to ConsensusFeature
cf.insert(map_index++, channel_value, element_index);
} // ! channel_iterator
// check if we keep this feature or if it contains low-intensity quantifications
if (remove_low_intensity_quantifications_ && hasLowIntensityReporter_(cf))
{
continue;
}
// check featureHandles are not empty
if (overall_intensity == 0)
{
cf.setMetaValue("all_empty", String("true"));
}
cf.setIntensity(overall_intensity);
consensus_map.push_back(cf);
// the tandem-scan in the order they appear in the experiment
++element_index;
}
} // ! Experiment iterator
/// add meta information to the map
registerChannelsInOutputMap_(consensus_map);
}
/// @brief extracts the iTRAQ channels from the MS data and stores intensity values in a consensus map
///
/// @param ms_exp_data Raw data to read
/// @param consensus_map Output each MS² scan as a consensus feature
/// @throws Exception::MissingInformation if no scans present or MS² scan has no precursor
void ItraqChannelExtractor::run(const MSExperiment<Peak1D>& ms_exp_data, ConsensusMap& consensus_map)
{
if (ms_exp_data.empty())
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Experiment has no scans!");
}
MSExperiment<> ms_exp_MS2;
String mode = (String) param_.getValue("select_activation");
std::cout << "Selecting scans with activation mode: " << (mode == "" ? "any" : mode) << "\n";
HasActivationMethod<MSExperiment<Peak1D>::SpectrumType> activation_predicate(ListUtils::create<String>(mode));
for (size_t idx = 0; idx < ms_exp_data.size(); ++idx)
{
if (ms_exp_data[idx].getMSLevel() == 2)
{
if (mode == "" || activation_predicate(ms_exp_data[idx]))
{
// copy only MS² scans
ms_exp_MS2.addSpectrum(ms_exp_data[idx]);
}
else
{
//std::cout << "deleting spectrum # " << idx << " with RT: " << ms_exp_data[idx].getRT() << "\n";
}
}
}
#ifdef ITRAQ_DEBUG
std::cout << "we have " << ms_exp_MS2.size() << " scans left of level " << ms_exp_MS2[0].getMSLevel() << std::endl;
std::cout << "run: channel_map_ has " << channel_map_.size() << " entries!" << std::endl;
#endif
consensus_map.clear(false);
// set <mapList> header
Int index_cnt = 0;
for (ChannelMapType::const_iterator cm_it = channel_map_.begin(); cm_it != channel_map_.end(); ++cm_it)
{
// structure of Map cm_it
// first == channel-name as Int e.g. 114
// second == ChannelInfo struct
ConsensusMap::FileDescription channel_as_map;
// label is the channel + description provided in the Params
if (itraq_type_ != TMT_SIXPLEX)
channel_as_map.label = "iTRAQ_" + String(cm_it->second.name) + "_" + String(cm_it->second.description);
else
channel_as_map.label = "TMT_" + String(cm_it->second.name) + "_" + String(cm_it->second.description);
channel_as_map.size = ms_exp_MS2.size();
//TODO what about .filename? leave empty?
// add some more MetaInfo
channel_as_map.setMetaValue("channel_name", cm_it->second.name);
channel_as_map.setMetaValue("channel_id", cm_it->second.id);
channel_as_map.setMetaValue("channel_description", cm_it->second.description);
channel_as_map.setMetaValue("channel_center", cm_it->second.center);
channel_as_map.setMetaValue("channel_active", String(cm_it->second.active ? "true" : "false"));
consensus_map.getFileDescriptions()[index_cnt++] = channel_as_map;
}
// create consensusElements
Peak2D::CoordinateType allowed_deviation = (Peak2D::CoordinateType) param_.getValue("reporter_mass_shift");
// now we have picked data
// --> assign peaks to channels
UInt element_index(0);
for (MSExperiment<>::ConstIterator it = ms_exp_MS2.begin(); it != ms_exp_MS2.end(); ++it)
{
// store RT&MZ of parent ion as centroid of ConsensusFeature
ConsensusFeature cf;
cf.setUniqueId();
cf.setRT(it->getRT());
if (it->getPrecursors().size() >= 1)
{
cf.setMZ(it->getPrecursors()[0].getMZ());
}
else
{
throw Exception::MissingInformation(__FILE__, __LINE__, __PRETTY_FUNCTION__, String("No precursor information given for scan native ID ") + String(it->getNativeID()) + " with RT " + String(it->getRT()));
}
Peak2D channel_value;
channel_value.setRT(it->getRT());
// for each each channel
Int index = 0;
Peak2D::IntensityType overall_intensity = 0;
for (ChannelMapType::const_iterator cm_it = channel_map_.begin(); cm_it != channel_map_.end(); ++cm_it)
{
// set mz-position of channel
channel_value.setMZ(cm_it->second.center);
// reset intensity
channel_value.setIntensity(0);
//add up all signals
for (MSExperiment<>::SpectrumType::ConstIterator mz_it =
it->MZBegin(cm_it->second.center - allowed_deviation)
; mz_it != it->MZEnd(cm_it->second.center + allowed_deviation)
; ++mz_it
)
{
channel_value.setIntensity(channel_value.getIntensity() + mz_it->getIntensity());
}
overall_intensity += channel_value.getIntensity();
// add channel to ConsensusFeature
cf.insert(index++, channel_value, element_index);
} // ! channel_iterator
// check featureHandles are not empty
if (overall_intensity == 0)
{
cf.setMetaValue("all_empty", String("true"));
}
cf.setIntensity(overall_intensity);
consensus_map.push_back(cf);
// the tandem-scan in the order they appear in the experiment
++element_index;
} // ! Experiment iterator
#ifdef ITRAQ_DEBUG
std::cout << "processed " << element_index << " scans" << std::endl;
#endif
consensus_map.setExperimentType("itraq");
return;
}