diff --git a/.github/workflows/r-conda.yml b/.github/workflows/r-conda.yml
index df449de7..83e314e3 100644
--- a/.github/workflows/r-conda.yml
+++ b/.github/workflows/r-conda.yml
@@ -28,10 +28,10 @@ jobs:
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Create conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: recetox-aplcms-dev
           auto-update-conda: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5eaeb04d..86437e55 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [dev] - unreleased
 ### Added
+- added tests for mzdata and mzxml formats [#216](https://github.com/RECETOX/recetox-aplcms/pull/216)
 ### Changed
 ### Removed
 
diff --git a/conda/environment-build.yaml b/conda/environment-build.yaml
index 7aa8c457..79fe67b9 100644
--- a/conda/environment-build.yaml
+++ b/conda/environment-build.yaml
@@ -7,4 +7,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
-  - r-base =4.2
+  - r-base
diff --git a/conda/environment-dev.yaml b/conda/environment-dev.yaml
index b43ea0e1..ba6f3754 100644
--- a/conda/environment-dev.yaml
+++ b/conda/environment-dev.yaml
@@ -4,11 +4,11 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - icu <=70.1
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach
diff --git a/conda/environment.yaml b/conda/environment.yaml
index 9c6626cc..3ab1060c 100644
--- a/conda/environment.yaml
+++ b/conda/environment.yaml
@@ -4,10 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - r-base =4.2
+  - r-base
   - r-mass
   - r-rgl
-  - bioconductor-mzR
+  - bioconductor-mzR ==2.28.0
   - r-splines2
   - r-doparallel
   - r-foreach
diff --git a/conda/meta.yaml b/conda/meta.yaml
index b64d4f5c..db4da355 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -21,10 +21,10 @@ build:
   
 requirements:
   host:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach
@@ -37,10 +37,10 @@ requirements:
     - r-tibble
 
   run:
-    - r-base =4.2
+    - r-base
     - r-mass
     - r-rgl
-    - bioconductor-mzR
+    - bioconductor-mzR ==2.28.0
     - r-splines2
     - r-doparallel
     - r-foreach
diff --git a/tests/remote-files/input.txt b/tests/remote-files/input.txt
index f955ef46..4afb4bf2 100644
--- a/tests/remote-files/input.txt
+++ b/tests/remote-files/input.txt
@@ -4,4 +4,6 @@ https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_06_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_07_shortened.mzML
 https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/RCX_08_shortened.mzML
-https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
\ No newline at end of file
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/single_eic.mzml
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/alg3.mzdata
+https://gitlab.ics.muni.cz/umsa/umsa-files/-/raw/master/testdata/recetox-aplcms/input/test_file.mzXML
\ No newline at end of file
diff --git a/tests/testdata/test0_copy.mzxml b/tests/testdata/test0_copy.mzxml
new file mode 100644
index 00000000..0be57236
--- /dev/null
+++ b/tests/testdata/test0_copy.mzxml
@@ -0,0 +1,12279 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">
+  <msRun scanCount="583" startTime="PT2125.86S" endTime="PT8081.98S">
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.raw"
+                fileType="RAWData"
+                fileSha1="6f65a1287b2d7522c5fb90a8a5304212b3568b67"/>
+    <parentFile fileName="file:////2016_Jan_12_QE2_47.mzXML"
+                fileType="processedData"
+                fileSha1="d9c6278c1c6a8f8ca6c69133bacd00efc5f2e706"/>
+    <msInstrument msInstrumentID="1">
+      <msManufacturer category="msManufacturer" value="Thermo Finnigan"/>
+      <msModel category="msModel" value="unknown"/>
+      <msIonisation category="msIonisation" value="NSI"/>
+      <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>
+      <msDetector category="msDetector" value="unknown"/>
+      <software type="acquisition" name="Xcalibur" version="2.6-264001/2.6.0.2640"/>
+    </msInstrument>
+    <dataProcessing centroided="1">
+      <processingOperation name="peak picking"/>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="processing" name="ReAdW" version="2015.1.0(build Jun 29 2015 14:09:50)"/>
+      <comment>type: conversion</comment>
+    </dataProcessing>
+    <dataProcessing>
+      <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>
+      <processingOperation name="Conversion to mzML"/>
+    </dataProcessing>
+    <scan num="10613"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="26"
+          polarity="+"
+          retentionTime="PT2125.86S"
+          lowMz="91.7452"
+          highMz="1020.45"
+          basePeakMz="624.329"
+          basePeakIntensity="39941"
+          totIonCurrent="290992"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="10611" precursorIntensity="123964" precursorCharge="2" activationMethod="HCD">624.29266819296</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="275"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">eJxzCHu/kQEIHNaWxTiA6PijE8D0ZrU+MJ2g7HIARB+6VdUAohMZfyWA6POfRMDySclzwPwtNxeC6WTGi2DzNl9bvwBEpwbNAvNX9ywAy6c9ngemdzssBstnsuSD6XM3KsF0lmAQmL682BWsLkvIWwFEP1LPPwDh3wDL7/ta+wDMd/4JpvdayoLdk6NoB9a3jsUK7N7cxQ5g/WvDksD8giQrsLpdfBFgupbZEKz+oJ082JzaYBEwf2NQLJjf1MQN5m97qwz2R7OVH5jeu+IChG/nDTZn7zxOMN3cBAmHxw3zwe5tbqsDq9sp8QVsf/ulR2D3b595Amx+921PsL4tkSxg9f2PZ4Dde6mgASQPAOoAb+o=</peaks>
+    </scan>
+    <scan num="11140"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="30"
+          polarity="+"
+          retentionTime="PT2169.75S"
+          lowMz="95.7689"
+          highMz="1163.47"
+          basePeakMz="208"
+          basePeakIntensity="78214.4"
+          totIonCurrent="393771"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="11139" precursorIntensity="161835" precursorCharge="2" activationMethod="HCD">673.80972467574</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="316"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">eJxzCP9omsDAwOCwTiWmAURHRS1WAPMdYx6A6GiVVQdA9Jp/6WA62swZLL7eVBzMj2FWB9MbAsIWgOjkJY5g/s0MHjA/Nc3UAURvfJkONjf18XEwf0PYVLC9aYk9YHufVKeD1aerSILN36GpBTYnk9kbov/be7B85v+/YPWfJdLA6rKPT4C4Z3UoWH2ey2Wwus2iv8DqChs7wPZecJ/KAKJLJouBxZ8nZIDVlTbuBotvkC4G09WH68Hqt7beA5vbcPIr2P6tX3LB7m3lWgRWd7CpDsIX2gA256CNBZhue9QApvf5JIH1tXPXgM3bWJsGpntWQ8LtMAsrmN/XLQixr/Y42F39l/PB5m4L6QDb33+7GszfGv0IzJ/o+hzi3mc6YPMnaf4Hi19rzgbbO0n3GVj93tLHIHUAs1mG8g==</peaks>
+    </scan>
+    <scan num="12331"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="70"
+          polarity="+"
+          retentionTime="PT2257.94S"
+          lowMz="84.0448"
+          highMz="974.46"
+          basePeakMz="86.0969"
+          basePeakIntensity="67235.6"
+          totIonCurrent="870037"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="12329" precursorIntensity="306036" precursorCharge="2" activationMethod="HCD">560.28000000000</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="676"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">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</peaks>
+    </scan>
+    <scan num="12577"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="29"
+          polarity="+"
+          retentionTime="PT2274.86S"
+          lowMz="129.102"
+          highMz="1040.46"
+          basePeakMz="208.483"
+          basePeakIntensity="59652.6"
+          totIonCurrent="297727"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="12575" precursorIntensity="280270" precursorCharge="2" activationMethod="HCD">650.29377969938</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="307"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">eJxzSFB2c2BgYHA4XW+dAKITkhYcANG7ykQWgPkt0x6A6HWzesHiyY8KwPSWY2fA4pktng0gesNuf7A5WXznweZs1roHFs/ih6h/qzAFLJ51eZcCWH35RwYQnc0sDqa3mN4C689Z/Rls7gY+QbC+POfFYPHd/R1g8eJHl8HmHuB3AJtT/JkBTG8Ungw2v8ypGSy/2ToOrK9KVQJszrqsM2D5WuEPYPG98lJgfr2wAVj/lmYHsLrmJh2wvzemZoHNadFYD3bfpnVFEH7QSjB9UOkXWH2r10QwfWjrHbB4B9N5sHk3E8LBdAfXbrB9m//IgulubSuwvRduJYH5PdlxYPu2Cv2G8D8HgOnbHXVg83p+J4Lltxx6CHZH/+8MSPhf0AfLT3C8DA6Xg1I7QPoAQxqA4w==</peaks>
+    </scan>
+    <scan num="13283"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="69"
+          polarity="+"
+          retentionTime="PT2322.17S"
+          lowMz="84.045"
+          highMz="1110.49"
+          basePeakMz="558.313"
+          basePeakIntensity="291157"
+          totIonCurrent="1.67825e+006"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="13280" precursorIntensity="681502" precursorCharge="2" activationMethod="HCD">558.31223543247</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="667"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">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</peaks>
+    </scan>
+    <scan num="13369"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="95"
+          polarity="+"
+          retentionTime="PT2327.56S"
+          lowMz="84.0448"
+          highMz="970.511"
+          basePeakMz="558.312"
+          basePeakIntensity="491436"
+          totIonCurrent="2.79016e+006"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="13366" precursorIntensity="1.38133e+006" precursorCharge="2" activationMethod="HCD">558.31220242555</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="889"
+             precision="64"
+             byteOrder="network"
+             contentType="m/z-int">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</peaks>
+    </scan>
+    <scan num="13493"
+          scanType="Full"
+          centroided="1"
+          msLevel="2"
+          peaksCount="103"
+          polarity="+"
+          retentionTime="PT2335.35S"
+          lowMz="101.071"
+          highMz="1087.69"
+          basePeakMz="129.102"
+          basePeakIntensity="148147"
+          totIonCurrent="1.4374e+006"
+          msInstrumentID="1">
+      <precursorMz precursorScanNum="13484" precursorIntensity="603212" precursorCharge="3" activationMethod="HCD">457.23000000000</precursorMz>
+      <peaks compressionType="zlib"
+             compressedLen="970"
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+  </index>
+  <indexOffset>1203724</indexOffset>
+  <sha1>184f263cfeb065c2c78d1bcb900bf9ebc18ecb8f</sha1>
+</mzXML>
diff --git a/tests/testthat/test-load.lcms.R b/tests/testthat/test-load.lcms.R
new file mode 100644
index 00000000..dd55f6ef
--- /dev/null
+++ b/tests/testthat/test-load.lcms.R
@@ -0,0 +1,39 @@
+create_test_case <- function(filename, mz_length, rt_length, intensities_length) {
+  list(
+    filename = filename,
+    expected_type = "list",
+    expected_lengths = c(mz = mz_length, rt = rt_length, intensities = intensities_length),
+    expected_num_na = c(mz = 0, rt = 0, intensities = 0)
+  )
+}
+
+patrick::with_parameters_test_that(
+  "test load.lcms reads different file types",
+  {
+    # Arrange: Set up test inputs
+    testdata <- file.path("..", "testdata")
+    input_path <- file.path(testdata, "input", filename)
+
+    # Act: Execute the function with the test inputs
+    data <- load.lcms(input_path)
+
+    # Assert: Verify the function output matches expected results
+    # Check that the function returns an object of the expected type
+    actual_type <- data
+    testthat::expect_type(actual_type, expected_type)
+    
+    # Check the lengths of the vectors in the list
+    actual_lengths <- lengths(data)
+    testthat::expect_equal(actual_lengths, expected_lengths)
+
+    # Check the number of NA values in each vector
+    actual_num_na <- sapply(data, function(x) sum(is.na(x)))
+    testthat::expect_equal(actual_num_na, expected_num_na)
+  },
+  
+  patrick::cases(
+    test_case_1 = create_test_case("RCX_06_shortened.mzML", 879476, 879476, 879476),
+    test_case_2 = create_test_case("test_file.mzXML", 9647575, 9647575, 9647575),
+    test_case_3 = create_test_case("alg3.mzdata", 543894, 543894, 543894)
+  )
+)
\ No newline at end of file