Read PASEF DDA MS2 precursor information

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsBackendTimsTof
 Title: Mass spectrometry Data Backend for Bruker TimsTOF Files
-Version: 0.1.2
+Version: 0.2.0
 Authors@R:
     c(person(given = "Johannes", family = "Rainer",
              email = "[email protected]",
@@ -10,6 +10,10 @@ Authors@R:
              email = "[email protected]",
              role = "aut",
              comment = c(ORCID = "0000-0001-9438-6909")),
+      person(given = "Roger", family = "Gine Bertomeu", 
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-0288-9619"),
+             role = "aut"),
       person(given = "Steffen", family = "Neumann",
              email = "[email protected]",
              role = "ctb",
@@ -48,4 +52,4 @@ BugReports: https://github.com/RforMassSpectrometry/MsBackendTimsTof/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendTimsTof
 biocViews: Infrastructure, MassSpectrometry, Metabolomics, DataImport
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2

NAMESPACE

@@ -4,8 +4,10 @@ export(MsBackendTimsTof)
 exportClasses(MsBackendTimsTof)
 exportMethods(length)
 importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpmapply)
 importFrom(BiocParallel,bpparam)
 importFrom(IRanges,NumericList)
+importFrom(MsCoreUtils,between)
 importFrom(MsCoreUtils,i2index)
 importFrom(MsCoreUtils,rbindFill)
 importFrom(S4Vectors,DataFrame)
@@ -19,11 +21,19 @@ importFrom(opentimsr,OpenTIMS)
 importFrom(opentimsr,opentims_set_threads)
 importFrom(opentimsr,query)
 importFrom(opentimsr,setup_bruker_so)
+importFrom(opentimsr,table2df)
 importFrom(stats,setNames)
 importFrom(utils,capture.output)
 importMethodsFrom(Spectra,backendInitialize)
+importMethodsFrom(Spectra,collisionEnergy)
 importMethodsFrom(Spectra,dataStorage)
+importMethodsFrom(Spectra,isolationWindowLowerMz)
+importMethodsFrom(Spectra,isolationWindowTargetMz)
+importMethodsFrom(Spectra,isolationWindowUpperMz)
 importMethodsFrom(Spectra,msLevel)
 importMethodsFrom(Spectra,peaksVariables)
+importMethodsFrom(Spectra,precursorCharge)
+importMethodsFrom(Spectra,precursorIntensity)
+importMethodsFrom(Spectra,precursorMz)
 importMethodsFrom(Spectra,spectraData)
 importMethodsFrom(Spectra,spectraVariables)

R/MsBackendTimsTof-functions.R

@@ -288,6 +288,11 @@ MsBackendTimsTof <- function() {
 # can we assume that tms@all_coulmns is the same for all the TimsTOF?
 .TIMSTOF_COLUMNS <- c("mz", "intensity", "tof", "inv_ion_mobility")
 
+.TIMSTOF_MS2_COLUMNS <- c("precursorMz", "precursorCharge",
+                          "precursorIntensity", "collisionEnergy",
+                          "isolationWindowLowerMz", "isolationWindowTargetMz",
+                          "isolationWindowUpperMz")
+
 #' @importFrom methods as
 #'
 #' @importFrom S4Vectors DataFrame
@@ -349,6 +354,19 @@ MsBackendTimsTof <- function() {
         res[["dataStorage"]] <- dataStorage(x)
         core_cols <- core_cols[core_cols != "dataStorage"]
     }
+    if (any(core_cols %in% .TIMSTOF_MS2_COLUMNS)) {
+        res_ms2_data <- .calculate_core_ms2_information(x)
+        for (col in core_cols[core_cols %in% .TIMSTOF_MS2_COLUMNS]) {
+            if (col == "precursorCharge"){
+                res[[col]] <- as.integer(
+                    res_ms2_data[, which(.TIMSTOF_MS2_COLUMNS == col)]
+                )
+            } else {
+                res[[col]] <- res_ms2_data[, which(.TIMSTOF_MS2_COLUMNS == col)]    
+            }
+            core_cols <- core_cols[core_cols != col]
+        }
+    }
     if (length(core_cols)) {
         res[core_cols] <- lapply(coreSpectraVariables()[core_cols],
                                  function(z, n) rep(as(NA, z), n), length(x))
@@ -357,3 +375,53 @@ MsBackendTimsTof <- function() {
         as(res, "DataFrame")
     else DataFrame()
 }
+
+#' @importFrom BiocParallel bpmapply bpparam
+.calculate_core_ms2_information <- function(x){
+    if (is.null(names(x@fileNames))){
+        return(matrix(numeric(), nrow = 0, ncol = length(.TIMSTOF_MS2_COLUMNS)))
+    }
+    tbls <- bpmapply(FUN = .do_calculate_core_ms2_information,
+                     x = names(x@fileNames),
+                     indices = lapply(split(x@indices[,1:2], f = x@indices[,3]),
+                                      matrix, ncol = 2),
+                     SIMPLIFY = FALSE,
+                     BPPARAM = bpparam())
+    output <- do.call(rbind, tbls)
+    output[order(order(x@indices[,3])), ]
+}
+
+#' @importFrom opentimsr OpenTIMS CloseTIMS table2df
+#' @importFrom MsCoreUtils between
+.do_calculate_core_ms2_information <- function(x, indices){
+    tms <- opentimsr::OpenTIMS(x)
+    on.exit(opentimsr::CloseTIMS(tms))
+    if (missing(indices)) {
+        indices <- unique(.query_tims(tms, frames = tms@frames$Id,
+                                      columns = c("frame", "scan")))
+    }
+    output <- matrix(NA_real_,
+                     nrow = nrow(indices),
+                     ncol = length(.TIMSTOF_MS2_COLUMNS))
+    tbl <- opentimsr::table2df(tms, c("PASEFFrameMsMsInfo", "Precursors"))
+    for (i in seq(nrow(tbl[[1]]))) {
+        row <- tbl[[1]][i, ]
+        prec <- tbl[[2]][row$Precursor,]
+        target_rows <- which(indices[,1] == row$Frame &
+                             MsCoreUtils::between(indices[,2],
+                                                  c(row$ScanNumBegin,
+                                                    row$ScanNumEnd)))
+        if (length(target_rows)) {
+            output[target_rows, ] <- 
+                rep(c(prec$MonoisotopicMz,                       ## precursorMz
+                         prec$Charge,                            ## precursorCharge
+                         prec$Intensity,                         ## precursorIntensity
+                         row$CollisionEnergy,                    ## collisionEnergy
+                         row$IsolationMz - row$IsolationWidth,   ## isolationWindowLowerMz
+                         row$IsolationMz,                        ## isolationWindowTargetMz
+                         row$IsolationMz + row$IsolationWidth),  ## isolationWindowUpperMz
+                     each = length(target_rows))
+        }
+    }
+    output
+}

R/MsBackendTimsTof.R

@@ -288,6 +288,62 @@ setMethod("msLevel", "MsBackendTimsTof", function(object, ...) {
     .get_msLevel(object)
 })
 
+#' @importMethodsFrom Spectra precursorMz
+#'
+#' @rdname MsBackendTimsTof
+setMethod("precursorMz", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "precursorMz"]
+})
+
+#' @importMethodsFrom Spectra precursorCharge
+#'
+#' @rdname MsBackendTimsTof
+setMethod("precursorCharge", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "precursorCharge"]
+})
+
+#' @importMethodsFrom Spectra precursorIntensity
+#'
+#' @rdname MsBackendTimsTof
+setMethod("precursorIntensity", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "precursorIntensity"]
+})
+
+#' @importMethodsFrom Spectra collisionEnergy
+#'
+#' @rdname MsBackendTimsTof
+setMethod("collisionEnergy", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "collisionEnergy"]
+})
+
+#' @importMethodsFrom Spectra isolationWindowLowerMz
+#'
+#' @rdname MsBackendTimsTof
+setMethod("isolationWindowLowerMz", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "isolationWindowLowerMz"]
+})
+
+#' @importMethodsFrom Spectra isolationWindowTargetMz
+#'
+#' @rdname MsBackendTimsTof
+setMethod("isolationWindowTargetMz", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "isolationWindowTargetMz"]
+})
+
+#' @importMethodsFrom Spectra isolationWindowUpperMz
+#'
+#' @rdname MsBackendTimsTof
+setMethod("isolationWindowUpperMz", "MsBackendTimsTof", function(object, ...) {
+    tbl <- .calculate_core_ms2_information(object)
+    tbl[, .TIMSTOF_MS2_COLUMNS == "isolationWindowUpperMz"]
+})
+
 #' @rdname MsBackendTimsTof
 setMethod("$", "MsBackendTimsTof", function(x, name) {
     if (!any(spectraVariables(x) == name))

tests/testthat/test_MsBackendTimsTof-functions.R

@@ -145,3 +145,18 @@ test_that(".inv_ion_mobility works", {
     res_2 <- .inv_ion_mobility(be_2)
     expect_equal(res_2, res[idx])
 })
+
+test_that("calculate_core_ms2_information works", {
+    tbl <- .calculate_core_ms2_information(be)
+    expect_true(is.numeric(tbl))
+    expect_equal(ncol(tbl), length(.TIMSTOF_MS2_COLUMNS))
+    expect_equal(nrow(tbl), nrow(be@indices))
+    expect_true(!all(is.na(tbl)))
+
+    #Check that it also works with subsets of scans
+    be_subset <- be[c(120:130, 17000:17010)] #From both file 1 and 2
+    tbl <- .calculate_core_ms2_information(be_subset)
+    expect_equal(ncol(tbl), length(.TIMSTOF_MS2_COLUMNS))
+    expect_equal(nrow(tbl), nrow(be_subset@indices))
+})
+

tests/testthat/test_MsBackendTimsTof.R

@@ -184,6 +184,48 @@ test_that("msLevel,MsBackendTimsTof works", {
     expect_identical(res, match(.get_frame_columns(be, "MsMsType"), c(0L, 8L)))
 })
 
+test_that("precursorMz,MsBackendTimsTof works", {
+    expect_identical(precursorMz(MsBackendTimsTof()), numeric(0))
+    res <- precursorMz(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("precursorCharge,MsBackendTimsTof works", {
+    expect_identical(precursorCharge(MsBackendTimsTof()), numeric(0))
+    res <- precursorCharge(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("precursorIntensity,MsBackendTimsTof works", {
+    expect_identical(precursorIntensity(MsBackendTimsTof()), numeric(0))
+    res <- precursorIntensity(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("collisionEnergy,MsBackendTimsTof works", {
+    expect_identical(collisionEnergy(MsBackendTimsTof()), numeric(0))
+    res <- collisionEnergy(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("isolationWindowLowerMz,MsBackendTimsTof works", {
+    expect_identical(isolationWindowLowerMz(MsBackendTimsTof()), numeric(0))
+    res <- isolationWindowLowerMz(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("isolationWindowTargetMz,MsBackendTimsTof works", {
+    expect_identical(isolationWindowTargetMz(MsBackendTimsTof()), numeric(0))
+    res <- isolationWindowTargetMz(be)
+    expect_identical(length(res), length(be))
+})
+
+test_that("isolationWindowUpperMz,MsBackendTimsTof works", {
+    expect_identical(isolationWindowUpperMz(MsBackendTimsTof()), numeric(0))
+    res <- isolationWindowUpperMz(be)
+    expect_identical(length(res), length(be))
+})
+
 test_that("$,MsBackendTimsTof works", {
     res_all <- spectraData(be)