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feat: extract electronBeamEnergy MS term #303

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Merged
sneumann merged 1 commit into from
Feb 6, 2025
Merged

feat: extract electronBeamEnergy MS term #303

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ Package: mzR
Type: Package
Title: parser for netCDF, mzXML and mzML and mzIdentML files
(mass spectrometry data)
Version: 2.41.1
Version: 2.41.2
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
Authors@R: c(
person("Steffen", "Neumann", email="[email protected]", role=c("aut","cre")),
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4 changes: 4 additions & 0 deletions NEWS
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@@ -1,3 +1,7 @@
CHANGES IN VERSION 2.41.2
-------------------------
o Report also electron beam energy (MS:1003410) for EAD data.

CHANGES IN VERSION 2.41.1
-------------------------
o Fix compilation error with stricter compiler checks
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2 changes: 2 additions & 0 deletions inst/unitTests/test_pwiz.R
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Expand Up @@ -20,6 +20,8 @@ test_mzXML <- function() {
checkTrue(any(colnames(hdr) == "scanWindowUpperLimit"))
checkTrue(all(!is.na(hdr$scanWindowLowerLimit)))
checkTrue(all(!is.na(hdr$scanWindowUpperLimit)))
checkTrue(any(colnames(hdr) == "electronBeamEnergy"))
checkTrue(all(is.na(hdr$electronBeamEnergy)))
hdr <- header(mzxml,1)
checkTrue(is.list(hdr))
hdr <- header(mzxml, 2:3)
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10 changes: 8 additions & 2 deletions src/RcppPwiz.cpp
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Expand Up @@ -200,7 +200,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
Rcpp::NumericVector isolationWindowUpperOffset(N_scans);
Rcpp::NumericVector scanWindowLowerLimit(N_scans);
Rcpp::NumericVector scanWindowUpperLimit(N_scans);

Rcpp::NumericVector electronBeamEnergy(N_scans);

for (size_t i = 0; i < N_scans; i++) {
int current_scan = whichScan[i];
size_t current_index = static_cast<size_t>(current_scan - 1);
Expand Down Expand Up @@ -262,6 +263,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
const Precursor& precursor = sp->precursors[0];
// collisionEnergy
collisionEnergy[i] = precursor.activation.cvParam(MS_collision_energy).valueAs<double>();
// electronBeamEnergy - for EAD
electronBeamEnergy[i] = precursor.activation.cvParam(MS_electron_beam_energy).value.empty() ? NA_REAL : precursor.activation.cvParam(MS_electron_beam_energy).valueAs<double>();
// precursorScanNum
size_t precursorIndex = slp->find(precursor.spectrumID);
if (precursorIndex < N) {
Expand All @@ -288,6 +291,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
}
} else {
collisionEnergy[i] = NA_REAL;
electronBeamEnergy[i] = NA_REAL;
precursorScanNum[i] = NA_INTEGER;
precursorMZ[i] = NA_REAL;
precursorCharge[i] = NA_INTEGER;
Expand All @@ -302,7 +306,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
}
}

Rcpp::List header(31);
Rcpp::List header(32);
std::vector<std::string> names;
size_t i = 0;
names.push_back("seqNum");
Expand Down Expand Up @@ -367,6 +371,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {
header[i++] = Rcpp::wrap(scanWindowLowerLimit);
names.push_back("scanWindowUpperLimit");
header[i++] = Rcpp::wrap(scanWindowUpperLimit);
names.push_back("electronBeamEnergy");
header[i++] = Rcpp::wrap(electronBeamEnergy);
header.attr("names") = names;

return header;
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