diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 3186216..9e5dfaf 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -39,6 +39,7 @@ env:
run_pkgdown: 'false'
has_RUnit: 'false'
cache-version: 'cache-v1'
+ run_docker: 'false'
jobs:
build-check:
@@ -48,12 +49,14 @@ jobs:
## Environment variables unique to this job.
strategy:
- fail-fast: false
+ fail-fast: false
matrix:
config:
- - { os: ubuntu-latest, r: '4.1.3', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- - { os: macOS-latest, r: '4.1.3', bioc: '3.14'}
- - { os: windows-latest, r: '4.1.3', bioc: '3.14'}
+ - { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+ - { os: macOS-latest, r: 'devel', bioc: '3.17'}
+ - { os: windows-latest, r: 'devel', bioc: '3.17'}
+ ## Check https://github.com/r-lib/actions/tree/master/examples
+ ## for examples using the http-user-agent
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
@@ -76,19 +79,20 @@ jobs:
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- name: Checkout Repository
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
if: runner.os != 'Linux'
- uses: r-lib/actions/setup-r@master
+ uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
## pandoc is already included in the Bioconductor docker images
- name: Setup pandoc from r-lib
if: runner.os != 'Linux'
- uses: r-lib/actions/setup-pandoc@master
+ uses: r-lib/actions/setup-pandoc@v2
- name: Query dependencies
run: |
@@ -96,31 +100,28 @@ jobs:
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
-
- - name: Cache R packages
+ - name: Restore R package cache
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
- uses: actions/cache@v2
+ uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
- key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3-
+ key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
- uses: actions/cache@v2
+ uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
- key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-r-4.1.3
+ key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+ restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
- name: Install Linux system dependencies
if: runner.os == 'Linux'
- ## sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
run: |
- sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y libicu-dev pandoc libpq-dev" )')
+ sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
-
- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
@@ -136,8 +137,11 @@ jobs:
## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi
- ## See if this helps get RCurl installed
- ## brew uninstall curl
+ ## For installing usethis's dependency gert
+ brew install libgit2
+
+ ## Required for tcltk
+ brew install xquartz --cask
- name: Install Windows system dependencies
if: runner.os == 'Windows'
@@ -153,10 +157,10 @@ jobs:
- name: Set BiocVersion
run: |
- BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+ BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
shell: Rscript {0}
- - name: Install dependencies
+ - name: Install dependencies pass 1
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
@@ -165,24 +169,37 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
- ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79
- remotes::install_github("ropensci/bibtex")
- remotes::install_github("ropensci/RefManageR")
- remotes::install_github("cboettig/knitcitations")
-
+ ## Set the repos source depending on the OS
+ ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
+ ## though based on https://bit.ly/bioc2021-package-binaries
+ ## the Azure link will be the main one going forward.
+ gha_repos <- if(
+ .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
+ ) c(
+ "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.17/bioc",
+ BiocManager::repositories()
+ ) else BiocManager::repositories()
+
+ ## For running the checks
+ message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+ install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
## Pass #1 at installing dependencies
+ ## This pass uses AnVIL-powered fast binaries
+ ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
+ ## The speed gains only apply to the docker builds.
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
- remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+ remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
+ continue-on-error: true
+ shell: Rscript {0}
+ - name: Install dependencies pass 2
+ run: |
## Pass #2 at installing dependencies
+ ## This pass does not use AnVIL and will thus update any packages
+ ## that have seen been updated in Bioconductor
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
- remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
-
- ## For running the checks
- message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
- remotes::install_cran("rcmdcheck")
- BiocManager::install("BiocCheck")
+ remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}
- name: Install BiocGenerics
@@ -201,7 +218,13 @@ jobs:
- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
- remotes::install_cran("pkgdown")
+ remotes::install_github("r-lib/pkgdown")
+ shell: Rscript {0}
+
+ - name: Install suggested packages
+ run: |
+ BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA"))
+ install.packages(c("rmarkdown", "RPostgres", "RMySQL"))
shell: Rscript {0}
- name: Session info
@@ -214,10 +237,12 @@ jobs:
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
+ DISPLAY: 99.0
run: |
+ options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
- args = c("--no-build-vignettes", "--no-manual", "--timings"),
- build_args = c("--no-manual", "--no-resave-data"),
+ args = c("--no-manual", "--no-vignettes", "--timings"),
+ build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
@@ -235,18 +260,14 @@ jobs:
shell: Rscript {0}
- name: Run BiocCheck
+ env:
+ DISPLAY: 99.0
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
- `no-check-namespace` = TRUE,
- `no-check-pkg-size` = TRUE,
- `no-check-file-size` = TRUE,
- `no-check-version-num` = TRUE,
`no-check-R-ver` = TRUE,
- `no-check-bioc-help` = TRUE,
- `no-check-dependencies` = TRUE
-
+ `no-check-bioc-help` = TRUE
)
shell: Rscript {0}
@@ -260,21 +281,47 @@ jobs:
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .
- - name: Deploy package
+ - name: Build pkgdown site
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
- run: |
- git config --local user.email "actions@github.com"
- git config --local user.name "GitHub Actions"
- Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
- shell: bash {0}
+ run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+ shell: Rscript {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
## at least one locally before this will work. This creates the gh-pages
## branch (erasing anything you haven't version controlled!) and
## makes the git history recognizable by pkgdown.
+ - name: Install deploy dependencies
+ if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+ run: |
+ apt-get update && apt-get -y install rsync
+
+ - name: Deploy pkgdown site to GitHub pages 🚀
+ if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+ uses: JamesIves/github-pages-deploy-action@releases/v4
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
+
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
- name: ${{ runner.os }}-biocversion-r-4.1.3-results
+ name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check
+
+ ## Note that DOCKER_PASSWORD is really a token for your dockerhub
+ ## account, not your actual dockerhub account password.
+ ## This comes from
+ ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
+ ## Check https://github.com/docker/build-push-action/tree/releases/v1
+ ## for more details.
+ - uses: docker/build-push-action@v1
+ if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
+ with:
+ username: ${{ secrets.DOCKER_USERNAME }}
+ password: ${{ secrets.DOCKER_PASSWORD }}
+ repository: computational-metabolomics/structtoolbox
+ tag_with_ref: true
+ tag_with_sha: true
+ tags: latest
diff --git a/DESCRIPTION b/DESCRIPTION
index e05871d..31b08b4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -61,7 +61,7 @@ Suggests:
RPostgres,
RMySQL
VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
biocViews: MassSpectrometry, Metabolomics, Software
Collate:
diff --git a/R/purityA-create-msp.R b/R/purityA-create-msp.R
index cac65a2..e8bf006 100644
--- a/R/purityA-create-msp.R
+++ b/R/purityA-create-msp.R
@@ -206,7 +206,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
if (!is.null(av_inter) && nrow(av_inter)>0){
- write.msp(grpd$mz[1], grpd$rt[1], grpid, NA, av_inter, metadata, metadata_cols, of, method,
+ write.msp(median(grpd$mz), median(grpd$rt), grpid, NA, av_inter, metadata, metadata_cols, of, method,
adduct_split, msp_schema, intensity_ra, include_adducts)
}
@@ -230,7 +230,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
if (!is.null(av_intra_j) && nrow(av_intra_j)>0){
- write.msp(grpd$mz[1], grpd$rt[1], grpid, fileid, av_intra_j, metadata, metadata_cols,
+ write.msp(median(grpd$mz), median(grpd$rt), grpid, fileid, av_intra_j, metadata, metadata_cols,
of, method, adduct_split, msp_schema, intensity_ra, include_adducts)
}
@@ -248,7 +248,7 @@ mspurity_to_msp <- function (pa, msp_file_pth=NULL, metadata=NULL, metadata_cols
if (!is.null(av_all) && nrow(av_all)>0){
- write.msp(grpd$mz[1], grpd$rt[1], grpid, NA, av_all, metadata, metadata_cols, of,
+ write.msp(median(grpd$mz), median(grpd$rt), grpid, NA, av_all, metadata, metadata_cols, of,
method, adduct_split, msp_schema, intensity_ra, include_adducts)
}
diff --git a/inst/extdata/tests/db/metab_compound_subset.sqlite b/inst/extdata/tests/db/metab_compound_subset.sqlite
old mode 100755
new mode 100644
diff --git a/inst/extdata/tests/external_annotations/probmetab.tsv b/inst/extdata/tests/external_annotations/probmetab.tsv
old mode 100755
new mode 100644
diff --git a/inst/extdata/tests/msp/all.msp b/inst/extdata/tests/msp/all.msp
index 6608cfd..2854303 100644
--- a/inst/extdata/tests/msp/all.msp
+++ b/inst/extdata/tests/msp/all.msp
@@ -1 +1,28 @@
-RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2
PK$NUM_PEAK: 2
PK$PEAK: m/z int. rel.int.
104.053237915039 16147574 100
133.031829833984 10814390 66.97
RECORD_TITLE: MZ:150.0582 | RT:62.3 | grpid:187 | file:2 | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906
AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 29.71
104.053276062012 13982832 100
133.031875610352 9440187 67.51
150.058349609375 1694299.125 12.12
\ No newline at end of file
+RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
+AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+104.053237915039 16147574 100
+133.031829833984 10814390 66.97
+
+RECORD_TITLE: MZ:150.0582 | RT:62.3 | grpid:187 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 29.71
+104.053276062012 13982832 100
+133.031875610352 9440187 67.51
+150.058349609375 1694299.125 12.12
+
diff --git a/inst/extdata/tests/msp/all_OLD.msp b/inst/extdata/tests/msp/all_OLD.msp
index 7b9dfd6..3b949df 100644
--- a/inst/extdata/tests/msp/all_OLD.msp
+++ b/inst/extdata/tests/msp/all_OLD.msp
@@ -1,84 +1,84 @@
-RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070816040039
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070892333984 100876.1328125 100
-
-RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070785522461
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 165623.640625 100
-
-RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070838928223
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070854187012 97631.5859375 100
-
-RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070831298828
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 1782171 100
-
-RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070770263672
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070922851562 149471.265625 100
-
-RECORD_TITLE: MZ:132.1019 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
-RECORD_TITLE: MZ:132.1019 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H+NH3]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
+RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070816040039
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070892333984 100876.1328125 100
+
+RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070785522461
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 165623.640625 100
+
+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070838928223
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070854187012 97631.5859375 100
+
+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070831298828
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 1782171 100
+
+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070770263672
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070922851562 149471.265625 100
+
+RECORD_TITLE: MZ:132.1019 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
+RECORD_TITLE: MZ:132.1019 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
diff --git a/inst/extdata/tests/msp/av_all.msp b/inst/extdata/tests/msp/av_all.msp
index 670acd7..ead3c4a 100644
--- a/inst/extdata/tests/msp/av_all.msp
+++ b/inst/extdata/tests/msp/av_all.msp
@@ -1 +1,15 @@
-RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:NA | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 13.79
104.053256988525 30130406 100
133.031852722168 20254577 67.22
150.058349609375 1694299.125 5.62
\ No newline at end of file
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 13.79
+104.053256988525 30130406 100
+133.031852722168 20254577 67.22
+150.058349609375 1694299.125 5.62
+
diff --git a/inst/extdata/tests/msp/av_all_OLD.msp b/inst/extdata/tests/msp/av_all_OLD.msp
index ac04d17..6022e08 100644
--- a/inst/extdata/tests/msp/av_all_OLD.msp
+++ b/inst/extdata/tests/msp/av_all_OLD.msp
@@ -1,12 +1,12 @@
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:NA | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 2295773.625 100
-
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 2295773.625 100
+
diff --git a/inst/extdata/tests/msp/av_all_dupmeta.msp b/inst/extdata/tests/msp/av_all_dupmeta.msp
index 53dbac2..379cfa5 100644
--- a/inst/extdata/tests/msp/av_all_dupmeta.msp
+++ b/inst/extdata/tests/msp/av_all_dupmeta.msp
@@ -1 +1,30 @@
-RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:NA | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 13.79
104.053256988525 30130406 100
133.031852722168 20254577 67.22
150.058349609375 1694299.125 5.62
RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:NA | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: possible other compound
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 13.79
104.053256988525 30130406 100
133.031852722168 20254577 67.22
150.058349609375 1694299.125 5.62
\ No newline at end of file
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 13.79
+104.053256988525 30130406 100
+133.031852722168 20254577 67.22
+150.058349609375 1694299.125 5.62
+
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: possible other compound
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 13.79
+104.053256988525 30130406 100
+133.031852722168 20254577 67.22
+150.058349609375 1694299.125 5.62
+
diff --git a/inst/extdata/tests/msp/av_all_dupmeta_OLD.msp b/inst/extdata/tests/msp/av_all_dupmeta_OLD.msp
index e894671..7816723 100644
--- a/inst/extdata/tests/msp/av_all_dupmeta_OLD.msp
+++ b/inst/extdata/tests/msp/av_all_dupmeta_OLD.msp
@@ -1,24 +1,24 @@
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:NA | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 2295773.625 100
-
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:NA | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: possible other compound
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 2295773.625 100
-
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 2295773.625 100
+
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: possible other compound
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 2295773.625 100
+
diff --git a/inst/extdata/tests/msp/av_inter.msp b/inst/extdata/tests/msp/av_inter.msp
index 9c5953a..7a78f86 100644
--- a/inst/extdata/tests/msp/av_inter.msp
+++ b/inst/extdata/tests/msp/av_inter.msp
@@ -1 +1,15 @@
-RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:NA | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 13.79
104.053256988525 30130406 100
133.031852722168 20254577 67.22
150.058349609375 1694299.125 5.62
\ No newline at end of file
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 13.79
+104.053256988525 30130406 100
+133.031852722168 20254577 67.22
+150.058349609375 1694299.125 5.62
+
diff --git a/inst/extdata/tests/msp/av_inter_OLD.msp b/inst/extdata/tests/msp/av_inter_OLD.msp
index a0683d7..eed684b 100644
--- a/inst/extdata/tests/msp/av_inter_OLD.msp
+++ b/inst/extdata/tests/msp/av_inter_OLD.msp
@@ -1,36 +1,36 @@
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:NA | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.07089805603 2295773.625 100
-
-RECORD_TITLE: MZ:132.1018 | RT:73.7 | grpid:27 | file:NA | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827230045
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
-RECORD_TITLE: MZ:132.1018 | RT:73.7 | grpid:27 | file:NA | adduct:[M+H+NH3]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827230045
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.07089805603 2295773.625 100
+
+RECORD_TITLE: MZ:132.1018 | RT:73.6 | grpid:27 | file:NA | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827517612
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.610979
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
+RECORD_TITLE: MZ:132.1018 | RT:73.6 | grpid:27 | file:NA | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827517612
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.610979
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
diff --git a/inst/extdata/tests/msp/av_intra.msp b/inst/extdata/tests/msp/av_intra.msp
index 7ef3301..9d7cd6a 100644
--- a/inst/extdata/tests/msp/av_intra.msp
+++ b/inst/extdata/tests/msp/av_intra.msp
@@ -1 +1,28 @@
-RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.19.2
PK$NUM_PEAK: 2
PK$PEAK: m/z int. rel.int.
104.053237915039 16147574 100
133.031829833984 10814390 66.97
RECORD_TITLE: MZ:150.0582 | RT:63.1 | grpid:187 | file:2 | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058155403723
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 29.71
104.053276062012 13982832 100
133.031875610352 9440187 67.51
150.058349609375 1694299.125 12.12
\ No newline at end of file
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+104.053237915039 16147574 100
+133.031829833984 10814390 66.97
+
+RECORD_TITLE: MZ:150.0582 | RT:62.7 | grpid:187 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058150670717
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.7001061862793
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 29.71
+104.053276062012 13982832 100
+133.031875610352 9440187 67.51
+150.058349609375 1694299.125 12.12
+
diff --git a/inst/extdata/tests/msp/av_intra_OLD.msp b/inst/extdata/tests/msp/av_intra_OLD.msp
index ac137be..2489cdb 100644
--- a/inst/extdata/tests/msp/av_intra_OLD.msp
+++ b/inst/extdata/tests/msp/av_intra_OLD.msp
@@ -1,48 +1,48 @@
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070896148682 266499.7734375 100
-
-RECORD_TITLE: MZ:116.0706 | RT:47.8 | grpid:12 | file:2 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070557825043
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 2029273.8515625 100
-
-RECORD_TITLE: MZ:132.1018 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827230045
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
-RECORD_TITLE: MZ:132.1018 | RT:73.7 | grpid:27 | file:1 | adduct:[M+H+NH3]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827230045
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070896148682 266499.7734375 100
+
+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:12 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070597631071
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.7384795
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 2029273.8515625 100
+
+RECORD_TITLE: MZ:132.1018 | RT:73.6 | grpid:27 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827517612
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.610979
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
+RECORD_TITLE: MZ:132.1018 | RT:73.6 | grpid:27 | file:1 | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827517612
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.610979
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
diff --git a/inst/extdata/tests/msp/max.msp b/inst/extdata/tests/msp/max.msp
index 2da19fb..12d83d2 100644
--- a/inst/extdata/tests/msp/max.msp
+++ b/inst/extdata/tests/msp/max.msp
@@ -1 +1,18 @@
-RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
CH$NAME: Methionine
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.19.2
PK$NUM_PEAK: 7
PK$PEAK: m/z int. rel.int.
102.055381774902 4631614.5 28.68
104.053237915039 16147574 100
105.000915527344 196574.15625 1.22
105.03719329834 273244.0625 1.69
133.031829833984 10814390 66.97
137.41633605957 30549.828125 0.19
150.058288574219 1973325.5 12.22
\ No newline at end of file
+RECORD_TITLE: MZ:150.0581 | RT:63.1 | grpid:187 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
+AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Methionine
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.21.2
+PK$NUM_PEAK: 7
+PK$PEAK: m/z int. rel.int.
+102.055381774902 4631614.5 28.68
+104.053237915039 16147574 100
+105.000915527344 196574.15625 1.22
+105.03719329834 273244.0625 1.69
+133.031829833984 10814390 66.97
+137.41633605957 30549.828125 0.19
+150.058288574219 1973325.5 12.22
+
diff --git a/inst/extdata/tests/msp/max_OLD.msp b/inst/extdata/tests/msp/max_OLD.msp
index 978f5f9..22422f9 100644
--- a/inst/extdata/tests/msp/max_OLD.msp
+++ b/inst/extdata/tests/msp/max_OLD.msp
@@ -1,38 +1,38 @@
-RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070823669434
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Sulfamethizole
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070892333984 1847702.625 100
-
-RECORD_TITLE: MZ:132.1019 | RT:73.5 | grpid:27 | file:2 | adduct:[M+H]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101867675781
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.11.4
-PK$NUM_PEAK: 2
-PK$PEAK: m/z int. rel.int.
-130.186950683594 121726.4453125 3.06
-132.102035522461 3973065.5 100
-
-RECORD_TITLE: MZ:132.1019 | RT:73.5 | grpid:27 | file:2 | adduct:[M+H+NH3]+
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101867675781
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-CH$NAME: Unknown
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.11.4
-PK$NUM_PEAK: 2
-PK$PEAK: m/z int. rel.int.
-130.186950683594 121726.4453125 3.06
-132.102035522461 3973065.5 100
-
+RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:12 | file:1 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070823669434
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Sulfamethizole
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070892333984 1847702.625 100
+
+RECORD_TITLE: MZ:132.1019 | RT:73.5 | grpid:27 | file:2 | adduct:[M+H]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101867675781
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.21.2
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+130.186950683594 121726.4453125 3.06
+132.102035522461 3973065.5 100
+
+RECORD_TITLE: MZ:132.1019 | RT:73.5 | grpid:27 | file:2 | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101867675781
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+CH$NAME: Unknown
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.21.2
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+130.186950683594 121726.4453125 3.06
+132.102035522461 3973065.5 100
+
diff --git a/inst/extdata/tests/msp/recrdt.msp b/inst/extdata/tests/msp/recrdt.msp
index dc9e566..b91e764 100644
--- a/inst/extdata/tests/msp/recrdt.msp
+++ b/inst/extdata/tests/msp/recrdt.msp
@@ -1 +1,26 @@
-RECORD_TITLE: Methionine
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2
PK$NUM_PEAK: 2
PK$PEAK: m/z int. rel.int.
104.053237915039 16147574 100
133.031829833984 10814390 66.97
RECORD_TITLE: Methionine
MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906
AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586
MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
XCMS groupid (grpid): 187
COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.19.2
PK$NUM_PEAK: 4
PK$PEAK: m/z int. rel.int.
102.055404663086 4154222.25 29.71
104.053276062012 13982832 100
133.031875610352 9440187 67.51
150.058349609375 1694299.125 12.12
\ No newline at end of file
+RECORD_TITLE: Methionine
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058135986328
+AC$CHROMATOGRAPHY: RETENTION_TIME 63.078168
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+104.053237915039 16147574 100
+133.031829833984 10814390 66.97
+
+RECORD_TITLE: Methionine
+MS$FOCUSED_ION: PRECURSOR_M/Z 150.058166503906
+AC$CHROMATOGRAPHY: RETENTION_TIME 62.3220443725586
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 187
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 4
+PK$PEAK: m/z int. rel.int.
+102.055404663086 4154222.25 29.71
+104.053276062012 13982832 100
+133.031875610352 9440187 67.51
+150.058349609375 1694299.125 12.12
+
diff --git a/inst/extdata/tests/msp/recrdt_OLD.msp b/inst/extdata/tests/msp/recrdt_OLD.msp
index b725ecc..4bb4dfd 100644
--- a/inst/extdata/tests/msp/recrdt_OLD.msp
+++ b/inst/extdata/tests/msp/recrdt_OLD.msp
@@ -1,77 +1,77 @@
-RECORD_TITLE: Sulfamethizole
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070816040039
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070892333984 100876.1328125 100
-
-RECORD_TITLE: Sulfamethizole
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070785522461
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 165623.640625 100
-
-RECORD_TITLE: Sulfamethizole
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070838928223
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070854187012 97631.5859375 100
-
-RECORD_TITLE: Sulfamethizole
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070831298828
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070899963379 1782171 100
-
-RECORD_TITLE: Sulfamethizole
-MS$FOCUSED_ION: PRECURSOR_M/Z 116.070770263672
-AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-116.070922851562 149471.265625 100
-
-RECORD_TITLE: Unknown
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
-RECORD_TITLE: Unknown
-MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
-AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
-MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
-AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
-XCMS groupid (grpid): 27
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.11.4
-PK$NUM_PEAK: 1
-PK$PEAK: m/z int. rel.int.
-132.101989746094 402822.6875 100
-
+RECORD_TITLE: Sulfamethizole
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070816040039
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070892333984 100876.1328125 100
+
+RECORD_TITLE: Sulfamethizole
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070785522461
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 165623.640625 100
+
+RECORD_TITLE: Sulfamethizole
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070838928223
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070854187012 97631.5859375 100
+
+RECORD_TITLE: Sulfamethizole
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070831298828
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070899963379 1782171 100
+
+RECORD_TITLE: Sulfamethizole
+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070770263672
+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+116.070922851562 149471.265625 100
+
+RECORD_TITLE: Unknown
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
+RECORD_TITLE: Unknown
+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101852416992
+AC$CHROMATOGRAPHY: RETENTION_TIME 73.692786
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+XCMS groupid (grpid): 27
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.21.2
+PK$NUM_PEAK: 1
+PK$PEAK: m/z int. rel.int.
+132.101989746094 402822.6875 100
+
diff --git a/tests/testthat/test.2_purityA_OLD.R b/tests/testthat/test.2_purityA_OLD.R
index aa85bc7..83d1c31 100644
--- a/tests/testthat/test.2_purityA_OLD.R
+++ b/tests/testthat/test.2_purityA_OLD.R
@@ -305,7 +305,6 @@ test_that("checking createMSP based functions (xcms v2 functions)", {
tmp_dir <- tempdir()
-
################################
# Check all method
################################
diff --git a/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd b/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd
index c8489fe..8fa5069 100644
--- a/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd
+++ b/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.Rmd
@@ -152,7 +152,7 @@ $$ F_{dpc} = \frac{\sum \vec{w_{Q} }\cdot \vec{w_{L}}}{\sqrt{\sum \vec{w_{Q}^{2}
The reverse dot product cosine (rpdc) uses the same algorithm as dpc but all peaks that do not match in the query spectra (based on the alignment) are omitted from the calculation. This will improve scores when the query spectra is noisy but should be used with caution as it might lead to more false positives.
-The composite dot product cosine (cdpc) approach is also calculated - this approach is used in the NIST MS search tool and incorporates relative intensity of neighbouring peaks (see function $M_{rel}$ ), where $N$=number of peaks, $Q$=query, $L$=library, $L\&Q$= matching library and query peaks, $w$ is the weighted value and $n$ is either 1 (if the abundance ratio of the library, i.e. $\frac{w_{L,i}}{w_{L,i-1}}$, is $<$ than the abundance ratio of the query i.e. $\frac{w_{Q,i}}{w_{Q,i-1}}$) or -1 (if the abundance ratio of the library is $>$ than the abundance ratio of the query). The approach was first described in [@stein1994optimization].
+The composite dot product cosine (cdpc) approach is also calculated - this approach is used in the NIST MS search tool and incorporates relative intensity of neighbouring peaks (see function $F_{rel}$ ), where $N$=number of peaks, $Q$=query, $L$=library, $L\&Q$= matching library and query peaks, $w$ is the weighted value and $n$ is either 1 (if the abundance ratio of the library, i.e. $\frac{w_{L,i}}{w_{L,i-1}}$, is $<$ than the abundance ratio of the query i.e. $\frac{w_{Q,i}}{w_{Q,i-1}}$) or -1 (if the abundance ratio of the library is $>$ than the abundance ratio of the query). The approach was first described in [@stein1994optimization].
$$ F_{rel} = \Bigg( \frac{1}{N_{L\&Q}-1} \Bigg) \cdot \sum_{i=2}^{N_{L\&Q}} \Bigg( \frac{w_{L,i}}{w_{L,i-1}} \Bigg)_{}{^n} \cdot \Bigg( \frac{w_{Q,i}}{w_{Q,i-1}} \Bigg)_{}{^{-n}}$$
diff --git a/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html b/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
index ec6d9d4..12261f6 100644
--- a/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
+++ b/vignettes/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html
@@ -11,41 +11,1287 @@
-
+
LC-MS/MS data processing and spectral matching workflow using msPurity and XCMS
-
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+h1.title {font-size: 38px;}
+h2 {font-size: 30px;}
+h3 {font-size: 24px;}
+h4 {font-size: 18px;}
+h5 {font-size: 16px;}
+h6 {font-size: 12px;}
+code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
+pre:not([class]) { background-color: white }
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+code{white-space: pre-wrap;}
+span.smallcaps{font-variant: small-caps;}
+span.underline{text-decoration: underline;}
+div.column{display: inline-block; vertical-align: top; width: 50%;}
+div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+ul.task-list{list-style: none;}
+
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+