diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index 486c6b227..32e8dd6fd 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -1351,35 +1351,28 @@ setMethod(
     "adjustRtime", signature(object = "MsExperiment",
                              param = "PeakGroupsParam"),
     function(object, param, msLevel = 1L, ...) {
+        if (!inherits(object, "XcmsExperiment"))
+            object <- as(object, "XcmsExperiment")
         if (hasAdjustedRtime(object)) {
             message("Removing previous alignment results")
             object <- dropAdjustedRtime(object)
         }
         if (any(msLevel != 1L))
             stop("Alignment is currently only supported for MS level 1")
-        if (!hasFeatures(object))
-            stop("No feature definitions present in 'object'. Please perform ",
-                 "first a correspondence analysis using 'groupChromPeaks'")
-        if (!nrow(peakGroupsMatrix(param)))
+        if (!nrow(peakGroupsMatrix(param))) {
+            if (!hasFeatures(object))
+                stop("No feature definitions present in 'object'. Please ",
+                     "perform first a correspondence analysis using ",
+                     "'groupChromPeaks'")
             peakGroupsMatrix(param) <- adjustRtimePeakGroups(
                 object, param = param)
+        }
         fidx <- as.factor(fromFile(object))
         rt_raw <- split(rtime(object), fidx)
-        rt_adj <- do_adjustRtime_peakGroups(
-            chromPeaks(object, msLevel = msLevel),
-            peakIndex = .update_feature_definitions(
-                featureDefinitions(object), rownames(chromPeaks(object)),
-                rownames(chromPeaks(object, msLevel = msLevel)))$peakidx,
-            rtime = rt_raw,
-            minFraction = minFraction(param),
-            extraPeaks = extraPeaks(param),
-            smooth = smooth(param),
-            span = span(param),
-            family = family(param),
-            peakGroupsMatrix = peakGroupsMatrix(param),
-            subset = subset(param),
-            subsetAdjust = subsetAdjust(param)
-        )
+        rt_adj <- .adjustRtime_peakGroupsMatrix(
+            rt_raw, peakGroupsMatrix(param), smooth = smooth(param),
+            span = span(param), family = family(param),
+            subset = subset(param), subsetAdjust = subsetAdjust(param))
         pt <- vapply(object@processHistory, processType, character(1))
         idx_pg <- .match_last(.PROCSTEP.PEAK.GROUPING, pt, nomatch = -1L)
         if (idx_pg > 0)
diff --git a/R/methods-XCMSnExp.R b/R/methods-XCMSnExp.R
index d95c49389..f46cc4cfc 100644
--- a/R/methods-XCMSnExp.R
+++ b/R/methods-XCMSnExp.R
@@ -1680,38 +1680,27 @@ setMethod("adjustRtime",
               }
               if (any(msLevel != 1))
                   stop("Alignment is currently only supported for MS level 1")
-              if (!hasChromPeaks(object))
-                  stop("No chromatographic peak detection results in 'object'!",
-                       " Please perform first a peak detection using the ",
-                       "'findChromPeaks' method.")
-              if (!hasFeatures(object))
-                  stop("No feature definitions found in 'object'! Please ",
-                       "perform first a peak grouping using the ",
-                       "'groupChromPeak' method.")
-              if (hasChromPeaks(object) & !.has_chrom_peak_data(object))
-                  object <- updateObject(object)
-              startDate <- date()
-              ## If param does contain a peakGroupsMatrix extract that one,
-              ## otherwise generate it.
               if (nrow(peakGroupsMatrix(param)))
                   pkGrpMat <- peakGroupsMatrix(param)
-              else
+              else {
+                  if (!hasChromPeaks(object))
+                      stop("No chromatographic peak detection results in ",
+                           "'object'! Please perform first a peak detection ",
+                           "using the 'findChromPeaks' method.")
+                  if (!hasFeatures(object))
+                      stop("No feature definitions found in 'object'! Please ",
+                           "perform first a peak grouping using the ",
+                           "'groupChromPeak' method.")
                   pkGrpMat <- adjustRtimePeakGroups(object, param = param)
-              res <- do_adjustRtime_peakGroups(
-                  chromPeaks(object, msLevel = msLevel),
-                  peakIndex = .update_feature_definitions(
-                      featureDefinitions(object), rownames(chromPeaks(object)),
-                      rownames(chromPeaks(object, msLevel = msLevel)))$peakidx,
-                  rtime = rtime(object, bySample = TRUE),
-                  minFraction = minFraction(param),
-                  extraPeaks = extraPeaks(param),
-                  smooth = smooth(param),
-                  span = span(param),
-                  family = family(param),
-                  peakGroupsMatrix = pkGrpMat,
-                  subset = subset(param),
-                  subsetAdjust = subsetAdjust(param)
-              )
+              }
+              if (hasChromPeaks(object) & !.has_chrom_peak_data(object))
+                  object <- updateObject(object)
+              startDate <- date()
+              res <- .adjustRtime_peakGroupsMatrix(
+                  rtime(object, bySample = TRUE), pkGrpMat,
+                  smooth = smooth(param), span = span(param),
+                  family = family(param), subset = subset(param),
+                  subsetAdjust = subsetAdjust(param))
               ## Add the pkGrpMat that's being used to the param object.
               peakGroupsMatrix(param) <- pkGrpMat
               ## Dropping the peak groups but don't remove its process history
diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R
index 1b47cc2f3..7a57d5d53 100644
--- a/tests/testthat/test_XcmsExperiment.R
+++ b/tests/testthat/test_XcmsExperiment.R
@@ -463,6 +463,15 @@ test_that("adjustRtime,MsExperiment,PeakGroupsParam works", {
     expect_true(length(res@processHistory) == 3L)
     expect_true(sum(rtime(res) != rtime(a)) > 1000)
 
+    ## Run with pre-defined anchor peak data
+    p <- res@processHistory[[3]]@param
+    res_2 <- adjustRtime(xmse, param = p)
+    expect_true(hasAdjustedRtime(res_2))
+    expect_equal(rtime(res), rtime(res_2))
+    res_2 <- adjustRtime(mse, param = p)
+    expect_true(hasAdjustedRtime(res_2))
+    expect_equal(rtime(res), rtime(res_2))
+
     ## Subset-based
     p <- PeakGroupsParam(span = 0.4, subset = c(1, 3))
     res_2 <- adjustRtime(a, p)
@@ -472,6 +481,14 @@ test_that("adjustRtime,MsExperiment,PeakGroupsParam works", {
     expect_true(sum(rtime(res_2) != rtime(a)) > 1000)
     expect_true(sum(rtime(res_2) != rtime(res)) > 1000)
 
+    ## Run with pre-defined anchor peak data
+    p <- res_2@processHistory[[3]]@param
+    res_3 <- adjustRtime(xmse, param = p)
+    expect_true(hasAdjustedRtime(res_3))
+    expect_equal(rtime(res_2), rtime(res_3))
+    res_3 <- adjustRtime(mse, param = p)
+    expect_true(hasAdjustedRtime(res_3))
+    expect_equal(rtime(res_2), rtime(res_3))
 })
 
 test_that("findChromPeaks,XcmsExperiment,MatchedFilterParam works", {
diff --git a/tests/testthat/test_methods-XCMSnExp.R b/tests/testthat/test_methods-XCMSnExp.R
index decf00e98..7e7d65b9f 100644
--- a/tests/testthat/test_methods-XCMSnExp.R
+++ b/tests/testthat/test_methods-XCMSnExp.R
@@ -1622,8 +1622,8 @@ test_that("adjustRtime,peakGroups works", {
     skip_on_os(os = "windows", arch = "i386")
 
     xod <- faahko_xod
-    xodg <- groupChromPeaks(xod,
-                            param = PeakDensityParam(sampleGroups = rep(1, 3)))
+    xodg <- groupChromPeaks(
+        xod, param = PeakDensityParam(sampleGroups = rep(1, 3)))
     pks <- chromPeaks(xodg)
     expect_true(length(processHistory(xodg,
                                       type = .PROCSTEP.PEAK.DETECTION)) == 1)