diff --git a/R/XcmsExperiment-functions.R b/R/XcmsExperiment-functions.R
index 050f4853..c306ac68 100644
--- a/R/XcmsExperiment-functions.R
+++ b/R/XcmsExperiment-functions.R
@@ -1168,8 +1168,8 @@ XcmsExperiment <- function() {
                             files = fileNames(from),
                             smoothed = NA)
     n@phenoData <- new("NAnnotatedDataFrame", as.data.frame(sampleData(from)))
-    fd <- as.data.frame(spectra(from)@backend@spectraData)
-    fd$fileIdx <- match(fd$dataStorage, fileNames(from))
+    fd <- as.data.frame(MsExperiment::spectra(from)@backend@spectraData)
+    fd$fileIdx <- match(fd$dataStorage, unique(fd$dataStorage))
     fd <- fd[, !colnames(fd) %in% c("dataStorage", "dataOrigin")]
     colnames(fd) <- sub("scanIndex", "spIdx", colnames(fd))
     colnames(fd) <- sub("rtime", "retentionTime", colnames(fd))
diff --git a/tests/testthat/test_XcmsExperiment-functions.R b/tests/testthat/test_XcmsExperiment-functions.R
index e79badd5..82ece278 100644
--- a/tests/testthat/test_XcmsExperiment-functions.R
+++ b/tests/testthat/test_XcmsExperiment-functions.R
@@ -210,7 +210,7 @@ test_that(".xcms_experiment_to_xcms_n_exp works", {
 
     a <- loadXcmsData("xmse")
     a1 <- a[1]
-    a1@spectra <- Spectra::setBackend(spectra(a1), MsBackendMemory())
+    a1@spectra <- Spectra::setBackend(spectra(a1), Spectra::MsBackendMemory())
     expect_error(xcms:::.xcms_experiment_to_xcms_n_exp(a1), "MsBackendMzR")
 
     res <- xcms:::.xcms_experiment_to_xcms_n_exp(a)