From c78c74be71984b2355a67786d464f1058a5190c2 Mon Sep 17 00:00:00 2001 From: emosca-cnr Date: Fri, 28 Jun 2024 18:17:56 +0200 Subject: [PATCH] v0.2.7 link to citation and zenodo --- DESCRIPTION | 4 +- NEWS | 8 +- README.md | 16 +- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/articles/margheRita.html | 99 +++--- docs/authors.html | 11 +- docs/index.html | 9 +- docs/pkgdown.yml | 2 +- docs/reference/CV_ratio.html | 2 +- docs/reference/Plot2DPCA.html | 2 +- docs/reference/RLA.html | 2 +- .../annotate_univariate_results.html | 2 +- .../as.PomaSummarizedExperiment.html | 2 +- docs/reference/as.metaboset.html | 2 +- docs/reference/calc_RI.html | 2 +- docs/reference/calc_ppm_err.html | 2 +- docs/reference/calc_reference.html | 2 +- docs/reference/check_RT.html | 2 +- docs/reference/check_RT_mass.html | 2 +- docs/reference/check_mass.html | 2 +- docs/reference/collapse_tech_rep.html | 2 +- docs/reference/filter_NA.html | 2 +- .../filter_metabolite_associations.html | 2 +- docs/reference/filtering.html | 2 +- .../get_spectra_list_from_vector.html | 2 +- docs/reference/h_map.html | 2 +- docs/reference/h_map_MSMS_comparison.html | 2 +- .../reference/heatscatter_chromatography.html | 2 +- docs/reference/imputation.html | 2 +- docs/reference/index.html | 2 +- .../keep_strongest_representative.html | 2 +- docs/reference/mL_demo.html | 2 +- docs/reference/mR_pca.html | 2 +- docs/reference/m_z_filtering.html | 2 +- docs/reference/mean_median_stdev_samples.html | 2 +- docs/reference/metab_boxplot.html | 2 +- docs/reference/metabolite_identification.html | 2 +- docs/reference/normalize_profiles.html | 2 +- docs/reference/pathway_analysis.html | 2 +- docs/reference/peak_matching.html | 2 +- docs/reference/pqn.html | 2 +- docs/reference/read_input_file.html | 2 +- docs/reference/remove_samples.html | 2 +- docs/reference/select_library.html | 2 +- docs/reference/select_sign_features.html | 2 +- docs/reference/size_effect.html | 2 +- docs/reference/splitQC.html | 2 +- docs/reference/univariate.html | 2 +- docs/reference/visualize_1spectra.html | 2 +- .../visualize_associated_spectra.html | 2 +- inst/CITATION | 6 +- inst/extdata/Urine_RP_NEG_norm_metadata.txt | 317 ++++++++++++++++++ inst/extdata/Urine_RP_POS_norm_metadata.txt | 317 ++++++++++++++++++ vignettes/margheRita.Rmd | 14 +- 55 files changed, 774 insertions(+), 117 deletions(-) create mode 100644 inst/extdata/Urine_RP_NEG_norm_metadata.txt create mode 100644 inst/extdata/Urine_RP_POS_norm_metadata.txt diff --git a/DESCRIPTION b/DESCRIPTION index 965e9c8..c6e678d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: margheRita Title: Mass spectrometry-based metabolomics data analysis -Version: 0.2.6 -Date: 2024-06-19 +Version: 0.2.7 +Date: 2024-06-28 Authors@R: c(person(given = "Ettore", family = "Mosca", role = c("aut", "cre"), email = "ettore.mosca@itb.cnr.it", comment = c(ORCID = "0000-0002-3102-5150")), person(given = "Zahrasadat", family = "Aalavikakhki", role = "aut", email = "zahrasadat.alavikakhki@studenti.unimi.it"), diff --git a/NEWS b/NEWS index 73a6098..c5068f3 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,10 @@ -03 May 2025, v0.2.5 +28 June 2024, v0.2.7 +-- addition of citation and link to zenodo dataset + +19 June 2024, v0.2.6 +-- various minor improvements in code, function documentation and vignettes + +03 May 2024, v0.2.5 -- various minor improvements in code, function documentation and vignettes 29 March 2024, v0.2.3 diff --git a/README.md b/README.md index 3dcdfd7..8d0cb05 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ Documentation: https://emosca-cnr.github.io/margheRita Source code: https://github.com/emosca-cnr/margheRita -Citation: ... +Citation: Ettore Mosca, Marynka Ulaszewska, Zahrasadat Alavikakhki, Edoardo Niccolò Bellini, Valeria Mannella, Gianfranco Frigerio, Denise Drago, Annapaola Andolfo. MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards. bioRxiv 2024.06.20.599545; doi: https://doi.org/10.1101/2024.06.20.599545 Contacts: @@ -27,17 +27,5 @@ Contacts: # Installation -The package requires a series of other R packages, which are availble in [CRAN](https://cran.r-project.org/), [Bioconductor](https://www.bioconductor.org/) and [github](https://github.com/). In most of the cases, the following instructions guarantee that all such dependencies are installed: - -```{r, eval=FALSE} -install.packages("devtools") -devtools::install_github(c("pcastellanoescuder/POMA", "antonvsdata/notame")) - -if (!require("BiocManager", quietly = TRUE)){ - install.packages("BiocManager") -} -BiocManager::install(c("clusterProfiler", "pcaMethods")) - -devtools::install_github("emosca-cnr/margheRita", dependencies = T) -``` +See documentation at https://emosca-cnr.github.io/margheRita diff --git a/docs/404.html b/docs/404.html index 69fed3c..d415d0c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/articles/index.html b/docs/articles/index.html index 3003e26..5d71db3 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/articles/margheRita.html b/docs/articles/margheRita.html index d28daa4..c78c4aa 100644 --- a/docs/articles/margheRita.html +++ b/docs/articles/margheRita.html @@ -33,7 +33,7 @@ margheRita - 0.2.6 + 0.2.7 @@ -105,6 +105,13 @@

Introductionhttps://github.com/emosca-cnr/margheRita

+

Citation: Ettore Mosca, Marynka Ulaszewska, Zahrasadat Alavikakhki, +Edoardo Niccolò Bellini, Valeria Mannella, Gianfranco Frigerio, Denise +Drago, Annapaola Andolfo. MargheRita: an R package for LC-MS/MS SWATH +metabolomics data analysis and confident metabolite identification based +on a spectral library of reference standards. bioRxiv 2024.06.20.599545; +doi: https://doi.org/10.1101/2024.06.20.599545

Contacts:

Documentation: https://emosca-cnr.github.io/margheRita

Source code: https://github.com/emosca-cnr/margheRita

-

Citation: …

+

Citation: Ettore Mosca, Marynka Ulaszewska, Zahrasadat Alavikakhki, Edoardo Niccolò Bellini, Valeria Mannella, Gianfranco Frigerio, Denise Drago, Annapaola Andolfo. MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards. bioRxiv 2024.06.20.599545; doi: https://doi.org/10.1101/2024.06.20.599545

Contacts:

  • @@ -87,10 +87,7 @@

    Installation

    -

    The package requires a series of other R packages, which are availble in CRAN, Bioconductor and github. In most of the cases, the following instructions guarantee that all such dependencies are installed:

    -

    ```{r, eval=FALSE} install.packages(“devtools”) devtools::install_github(c(“pcastellanoescuder/POMA”, “antonvsdata/notame”))

    -

    if (!require(“BiocManager”, quietly = TRUE)){ install.packages(“BiocManager”) } BiocManager::install(c(“clusterProfiler”, “pcaMethods”))

    -

    devtools::install_github(“emosca-cnr/margheRita”, dependencies = T) ```

    +

    See documentation at https://emosca-cnr.github.io/margheRita

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 294e61e..32e4165 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: margheRita: margheRita.html -last_built: 2024-06-19T14:05Z +last_built: 2024-06-28T16:15Z diff --git a/docs/reference/CV_ratio.html b/docs/reference/CV_ratio.html index 1232bf7..83b709e 100644 --- a/docs/reference/CV_ratio.html +++ b/docs/reference/CV_ratio.html @@ -21,7 +21,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/Plot2DPCA.html b/docs/reference/Plot2DPCA.html index 87950a0..e8b3882 100644 --- a/docs/reference/Plot2DPCA.html +++ b/docs/reference/Plot2DPCA.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/RLA.html b/docs/reference/RLA.html index 2e198e9..b649c11 100644 --- a/docs/reference/RLA.html +++ b/docs/reference/RLA.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/annotate_univariate_results.html b/docs/reference/annotate_univariate_results.html index c7ea659..b644c4e 100644 --- a/docs/reference/annotate_univariate_results.html +++ b/docs/reference/annotate_univariate_results.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/as.PomaSummarizedExperiment.html b/docs/reference/as.PomaSummarizedExperiment.html index 720ec69..629faf3 100644 --- a/docs/reference/as.PomaSummarizedExperiment.html +++ b/docs/reference/as.PomaSummarizedExperiment.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/as.metaboset.html b/docs/reference/as.metaboset.html index 47dfc31..058c330 100644 --- a/docs/reference/as.metaboset.html +++ b/docs/reference/as.metaboset.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/calc_RI.html b/docs/reference/calc_RI.html index d2b0455..20c0a4e 100644 --- a/docs/reference/calc_RI.html +++ b/docs/reference/calc_RI.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/calc_ppm_err.html b/docs/reference/calc_ppm_err.html index aced8cc..7772897 100644 --- a/docs/reference/calc_ppm_err.html +++ b/docs/reference/calc_ppm_err.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/calc_reference.html b/docs/reference/calc_reference.html index c2bfa3d..5689a24 100644 --- a/docs/reference/calc_reference.html +++ b/docs/reference/calc_reference.html @@ -18,7 +18,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/check_RT.html b/docs/reference/check_RT.html index fd73c83..ef6630e 100644 --- a/docs/reference/check_RT.html +++ b/docs/reference/check_RT.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/check_RT_mass.html b/docs/reference/check_RT_mass.html index d904f78..808b7d1 100644 --- a/docs/reference/check_RT_mass.html +++ b/docs/reference/check_RT_mass.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/check_mass.html b/docs/reference/check_mass.html index f4b26e9..9395144 100644 --- a/docs/reference/check_mass.html +++ b/docs/reference/check_mass.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/collapse_tech_rep.html b/docs/reference/collapse_tech_rep.html index d29a95c..0292946 100644 --- a/docs/reference/collapse_tech_rep.html +++ b/docs/reference/collapse_tech_rep.html @@ -18,7 +18,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/filter_NA.html b/docs/reference/filter_NA.html index a3e2e41..7047127 100644 --- a/docs/reference/filter_NA.html +++ b/docs/reference/filter_NA.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/filter_metabolite_associations.html b/docs/reference/filter_metabolite_associations.html index 0aaf81c..0ae98a3 100644 --- a/docs/reference/filter_metabolite_associations.html +++ b/docs/reference/filter_metabolite_associations.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/filtering.html b/docs/reference/filtering.html index 6b845ee..11b1d97 100644 --- a/docs/reference/filtering.html +++ b/docs/reference/filtering.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/get_spectra_list_from_vector.html b/docs/reference/get_spectra_list_from_vector.html index 64a0586..6ee963e 100644 --- a/docs/reference/get_spectra_list_from_vector.html +++ b/docs/reference/get_spectra_list_from_vector.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/h_map.html b/docs/reference/h_map.html index 576c708..9ea8bdd 100644 --- a/docs/reference/h_map.html +++ b/docs/reference/h_map.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/h_map_MSMS_comparison.html b/docs/reference/h_map_MSMS_comparison.html index a850fc4..2220191 100644 --- a/docs/reference/h_map_MSMS_comparison.html +++ b/docs/reference/h_map_MSMS_comparison.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/heatscatter_chromatography.html b/docs/reference/heatscatter_chromatography.html index 9db6b2a..191bf4a 100644 --- a/docs/reference/heatscatter_chromatography.html +++ b/docs/reference/heatscatter_chromatography.html @@ -20,7 +20,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/imputation.html b/docs/reference/imputation.html index b2fdea7..e880749 100644 --- a/docs/reference/imputation.html +++ b/docs/reference/imputation.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/index.html b/docs/reference/index.html index cbfbcba..352019c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/keep_strongest_representative.html b/docs/reference/keep_strongest_representative.html index 379d8bb..9a67832 100644 --- a/docs/reference/keep_strongest_representative.html +++ b/docs/reference/keep_strongest_representative.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/mL_demo.html b/docs/reference/mL_demo.html index 2554b00..e4874b8 100644 --- a/docs/reference/mL_demo.html +++ b/docs/reference/mL_demo.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/mR_pca.html b/docs/reference/mR_pca.html index 03f63f7..e56bfb2 100644 --- a/docs/reference/mR_pca.html +++ b/docs/reference/mR_pca.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/m_z_filtering.html b/docs/reference/m_z_filtering.html index 25e3ae4..85aefa8 100644 --- a/docs/reference/m_z_filtering.html +++ b/docs/reference/m_z_filtering.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/mean_median_stdev_samples.html b/docs/reference/mean_median_stdev_samples.html index 8780482..5f8c013 100644 --- a/docs/reference/mean_median_stdev_samples.html +++ b/docs/reference/mean_median_stdev_samples.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/metab_boxplot.html b/docs/reference/metab_boxplot.html index 10c49cb..6108161 100644 --- a/docs/reference/metab_boxplot.html +++ b/docs/reference/metab_boxplot.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/metabolite_identification.html b/docs/reference/metabolite_identification.html index 892cf5b..f1e043f 100644 --- a/docs/reference/metabolite_identification.html +++ b/docs/reference/metabolite_identification.html @@ -20,7 +20,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/normalize_profiles.html b/docs/reference/normalize_profiles.html index 81ec9bc..c8edf52 100644 --- a/docs/reference/normalize_profiles.html +++ b/docs/reference/normalize_profiles.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/pathway_analysis.html b/docs/reference/pathway_analysis.html index 46e9ee2..2fbbe8c 100644 --- a/docs/reference/pathway_analysis.html +++ b/docs/reference/pathway_analysis.html @@ -20,7 +20,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/peak_matching.html b/docs/reference/peak_matching.html index 99ec26e..7169343 100644 --- a/docs/reference/peak_matching.html +++ b/docs/reference/peak_matching.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/pqn.html b/docs/reference/pqn.html index d6a7eb4..65b7473 100644 --- a/docs/reference/pqn.html +++ b/docs/reference/pqn.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/read_input_file.html b/docs/reference/read_input_file.html index 961a7d6..d31957e 100644 --- a/docs/reference/read_input_file.html +++ b/docs/reference/read_input_file.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/remove_samples.html b/docs/reference/remove_samples.html index a6f89e1..a91bf9e 100644 --- a/docs/reference/remove_samples.html +++ b/docs/reference/remove_samples.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/select_library.html b/docs/reference/select_library.html index 39f6cec..68552fc 100644 --- a/docs/reference/select_library.html +++ b/docs/reference/select_library.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/select_sign_features.html b/docs/reference/select_sign_features.html index 1b99eee..82c9a96 100644 --- a/docs/reference/select_sign_features.html +++ b/docs/reference/select_sign_features.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/size_effect.html b/docs/reference/size_effect.html index e342e13..1baa81f 100644 --- a/docs/reference/size_effect.html +++ b/docs/reference/size_effect.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/splitQC.html b/docs/reference/splitQC.html index 9a5fc27..e8afa63 100644 --- a/docs/reference/splitQC.html +++ b/docs/reference/splitQC.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/univariate.html b/docs/reference/univariate.html index 044da2c..e9ad4e9 100644 --- a/docs/reference/univariate.html +++ b/docs/reference/univariate.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/visualize_1spectra.html b/docs/reference/visualize_1spectra.html index fa08700..5205145 100644 --- a/docs/reference/visualize_1spectra.html +++ b/docs/reference/visualize_1spectra.html @@ -17,7 +17,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/docs/reference/visualize_associated_spectra.html b/docs/reference/visualize_associated_spectra.html index 7df3f8a..e151bd8 100644 --- a/docs/reference/visualize_associated_spectra.html +++ b/docs/reference/visualize_associated_spectra.html @@ -20,7 +20,7 @@ margheRita - 0.2.6 + 0.2.7 diff --git a/inst/CITATION b/inst/CITATION index 366b08b..6bbeb73 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,7 +1,9 @@ bibentry( - bibtype = "misc", + bibtype = "article", title = "MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards", author = "Ettore Mosca and Marynka Ulaszewska and Edoardo Niccolò Bellini and Zahrasadat Alavikakhki and Gianfranco Frigerio and Denise Drago and Valeria Mannella and Annapaola Andolfo", + journal = "bioRxiv", year = "2024", - note = "R package version 0.2.3" + publisher = "Cold Spring Harbor Laboratory", + doi = "10.1101/2024.06.20.599545" ) diff --git a/inst/extdata/Urine_RP_NEG_norm_metadata.txt b/inst/extdata/Urine_RP_NEG_norm_metadata.txt new file mode 100644 index 0000000..05dc739 --- /dev/null +++ b/inst/extdata/Urine_RP_NEG_norm_metadata.txt @@ -0,0 +1,317 @@ +id injection_order batch class technical_rep biological_rep +x001_Blank_1_norm_RP_short_SWATH_neg 1 1 Blank 1 Blank +x002_Blank_1_norm_RP_short_SWATH_neg 2 1 Blank 1 Blank +x003_Blank_1_norm_RP_short_SWATH_neg 3 1 Blank 1 Blank +x004_QC_norm_equil_01_RP_short_SWATH_neg 4 1 QC 1 QC_equil_1 +x005_QC_norm_equil_02_RP_short_SWATH_neg 5 1 QC 2 QC_equil_2 +x006_QC_norm_equil_03_RP_short_SWATH_neg 6 1 QC 3 QC_equil_3 +x007_QC_norm_equil_04_RP_short_SWATH_neg 7 1 QC 4 QC_equil_4 +x008_QC_norm_equil_05_RP_short_SWATH_neg 8 1 QC 5 QC_equil_5 +x009_QC_norm_01_RP_short_SWATH_neg 9 1 QC 1 QC +x010_QC_norm_02_RP_short_SWATH_neg 10 1 QC 2 QC +x011_QC_norm_03_RP_short_SWATH_neg 11 1 QC 3 QC +x012_QC_norm_04_RP_short_SWATH_neg 12 1 QC 4 QC +x013_QC_norm_05_RP_short_SWATH_neg 13 1 QC 5 QC +x014_UR_norm_DD_mealC_t07_rtech1_RP_short_SWATH_neg 14 1 DD 1 mealC_t07 +x015_UR_norm_MM_mealB_t00_rtech1_RP_short_SWATH_neg 15 1 MM 1 mealB_t00 +x016_UR_norm_AA_mealA_t00_rtech1_RP_short_SWATH_neg 16 1 AA 1 mealA_t00 +x017_UR_norm_AA_mealC_t01_rtech1_RP_short_SWATH_neg 17 1 AA 1 mealC_t01 +x018_UR_norm_DD_mealA_t06_rtech1_RP_short_SWATH_neg 18 1 DD 1 mealA_t06 +x019_UR_norm_MM_mealC_t08_rtech1_RP_short_SWATH_neg 19 1 MM 1 mealC_t08 +x020_UR_norm_DD_mealA_t01_rtech1_RP_short_SWATH_neg 20 1 DD 1 mealA_t01 +x021_UR_norm_AA_mealC_t02_rtech1_RP_short_SWATH_neg 21 1 AA 1 mealC_t02 +x022_UR_norm_DD_mealA_t05_rtech1_RP_short_SWATH_neg 22 1 DD 1 mealA_t05 +x023_UR_norm_DD_mealC_t00_rtech1_RP_short_SWATH_neg 23 1 DD 1 mealC_t00 +x024_QC_norm_06_RP_short_SWATH_neg 24 1 QC 6 QC +x025_QC_norm_07_RP_short_SWATH_neg 25 1 QC 7 QC +x026_UR_norm_MM_mealA_t08_rtech1_RP_short_SWATH_neg 26 1 MM 1 mealA_t08 +x027_UR_norm_DD_mealB_t08_rtech1_RP_short_SWATH_neg 27 1 DD 1 mealB_t08 +x028_UR_norm_MM_mealA_t01_rtech1_RP_short_SWATH_neg 28 1 MM 1 mealA_t01 +x029_UR_norm_AA_mealA_t01_rtech1_RP_short_SWATH_neg 29 1 AA 1 mealA_t01 +x030_UR_norm_AA_mealB_t04_rtech1_RP_short_SWATH_neg 30 1 AA 1 mealB_t04 +x031_UR_norm_AA_mealB_t03_rtech1_RP_short_SWATH_neg 31 1 AA 1 mealB_t03 +x032_UR_norm_DD_mealC_t05_rtech1_RP_short_SWATH_neg 32 1 DD 1 mealC_t05 +x033_UR_norm_AA_mealC_t00_rtech1_RP_short_SWATH_neg 33 1 AA 1 mealC_t00 +x034_UR_norm_MM_mealB_t07_rtech1_RP_short_SWATH_neg 34 1 MM 1 mealB_t07 +x035_UR_norm_MM_mealA_t02_rtech1_RP_short_SWATH_neg 35 1 MM 1 mealA_t02 +x036_QC_norm_08_RP_short_SWATH_neg 36 1 QC 8 QC +x037_QC_norm_09_RP_short_SWATH_neg 37 1 QC 9 QC +x038_UR_norm_DD_mealC_t01_rtech1_RP_short_SWATH_neg 38 1 DD 1 mealC_t01 +x039_UR_norm_DD_mealA_t00_rtech1_RP_short_SWATH_neg 39 1 DD 1 mealA_t00 +x040_UR_norm_DD_mealA_t03_rtech1_RP_short_SWATH_neg 40 1 DD 1 mealA_t03 +x041_UR_norm_DD_mealC_t03_rtech1_RP_short_SWATH_neg 41 1 DD 1 mealC_t03 +x042_UR_norm_AA_mealA_t04_rtech1_RP_short_SWATH_neg 42 1 AA 1 mealA_t04 +x043_UR_norm_AA_mealB_t08_rtech1_RP_short_SWATH_neg 43 1 AA 1 mealB_t08 +x044_UR_norm_AA_mealB_t01_rtech1_RP_short_SWATH_neg 44 1 AA 1 mealB_t01 +x045_UR_norm_AA_mealB_t05_rtech1_RP_short_SWATH_neg 45 1 AA 1 mealB_t05 +x046_UR_norm_MM_mealC_t04_rtech1_RP_short_SWATH_neg 46 1 MM 1 mealC_t04 +x047_UR_norm_MM_mealC_t02_rtech1_RP_short_SWATH_neg 47 1 MM 1 mealC_t02 +x048_QC_norm_10_RP_short_SWATH_neg 48 1 QC 10 QC +x049_QC_norm_11_RP_short_SWATH_neg 49 1 QC 11 QC +x050_UR_norm_MM_mealA_t07_rtech1_RP_short_SWATH_neg 50 1 MM 1 mealA_t07 +x051_UR_norm_DD_mealB_t02_rtech1_RP_short_SWATH_neg 51 1 DD 1 mealB_t02 +x052_UR_norm_MM_mealC_t07_rtech1_RP_short_SWATH_neg 52 1 MM 1 mealC_t07 +x053_UR_norm_DD_mealB_t07_rtech1_RP_short_SWATH_neg 53 1 DD 1 mealB_t07 +x054_UR_norm_MM_mealC_t01_rtech1_RP_short_SWATH_neg 54 1 MM 1 mealC_t01 +x055_UR_norm_DD_mealA_t04_rtech1_RP_short_SWATH_neg 55 1 DD 1 mealA_t04 +x056_UR_norm_MM_mealB_t05_rtech1_RP_short_SWATH_neg 56 1 MM 1 mealB_t05 +x057_UR_norm_DD_mealB_t05_rtech1_RP_short_SWATH_neg 57 1 DD 1 mealB_t05 +x058_UR_norm_AA_mealA_t07_rtech1_RP_short_SWATH_neg 58 1 AA 1 mealA_t07 +x059_UR_norm_AA_mealA_t05_rtech1_RP_short_SWATH_neg 59 1 AA 1 mealA_t05 +x060_QC_norm_12_RP_short_SWATH_neg 60 1 QC 12 QC +x061_UR_norm_MM_mealB_t04_rtech1_RP_short_SWATH_neg 61 1 MM 1 mealB_t04 +x062_UR_norm_MM_mealB_t06_rtech1_RP_short_SWATH_neg 62 1 MM 1 mealB_t06 +x063_UR_norm_AA_mealB_t07_rtech1_RP_short_SWATH_neg 63 1 AA 1 mealB_t07 +x064_UR_norm_MM_mealC_t03_rtech1_RP_short_SWATH_neg 64 1 MM 1 mealC_t03 +x065_UR_norm_MM_mealC_t05_rtech1_RP_short_SWATH_neg 65 1 MM 1 mealC_t05 +x066_UR_norm_MM_mealA_t03_rtech1_RP_short_SWATH_neg 66 1 MM 1 mealA_t03 +x067_UR_norm_DD_mealB_t04_rtech1_RP_short_SWATH_neg 67 1 DD 1 mealB_t04 +x068_UR_norm_AA_mealC_t07_rtech1_RP_short_SWATH_neg 68 1 AA 1 mealC_t07 +x069_UR_norm_AA_mealC_t05_rtech1_RP_short_SWATH_neg 69 1 AA 1 mealC_t05 +x070_UR_norm_MM_mealA_t05_rtech1_RP_short_SWATH_neg 70 1 MM 1 mealA_t05 +x071_QC_norm_13_RP_short_SWATH_neg 71 1 QC 13 QC +x072_QC_norm_14_RP_short_SWATH_neg 72 1 QC 14 QC +x073_UR_norm_MM_mealB_t03_rtech1_RP_short_SWATH_neg 73 1 MM 1 mealB_t03 +x074_UR_norm_DD_mealB_t00_rtech1_RP_short_SWATH_neg 74 1 DD 1 mealB_t00 +x075_UR_norm_MM_mealC_t06_rtech1_RP_short_SWATH_neg 75 1 MM 1 mealC_t06 +x076_UR_norm_AA_mealA_t06_rtech1_RP_short_SWATH_neg 76 1 AA 1 mealA_t06 +x077_UR_norm_DD_mealC_t04_rtech1_RP_short_SWATH_neg 77 1 DD 1 mealC_t04 +x078_UR_norm_AA_mealB_t06_rtech1_RP_short_SWATH_neg 78 1 AA 1 mealB_t06 +x079_UR_norm_DD_mealA_t02_rtech1_RP_short_SWATH_neg 79 1 DD 1 mealA_t02 +x080_UR_norm_DD_mealB_t03_rtech1_RP_short_SWATH_neg 80 1 DD 1 mealB_t03 +x081_UR_norm_AA_mealA_t08_rtech1_RP_short_SWATH_neg 81 1 AA 1 mealA_t08 +x082_UR_norm_AA_mealC_t04_rtech1_RP_short_SWATH_neg 82 1 AA 1 mealC_t04 +x083_QC_norm_15_RP_short_SWATH_neg 83 1 QC 15 QC +x084_QC_norm_16_RP_short_SWATH_neg 84 1 QC 16 QC +x085_UR_norm_AA_mealC_t08_rtech1_RP_short_SWATH_neg 85 1 AA 1 mealC_t08 +x086_UR_norm_MM_mealA_t06_rtech1_RP_short_SWATH_neg 86 1 MM 1 mealA_t06 +x087_UR_norm_AA_mealA_t03_rtech1_RP_short_SWATH_neg 87 1 AA 1 mealA_t03 +x088_UR_norm_AA_mealC_t03_rtech1_RP_short_SWATH_neg 88 1 AA 1 mealC_t03 +x089_UR_norm_DD_mealA_t08_rtech1_RP_short_SWATH_neg 89 1 DD 1 mealA_t08 +x090_UR_norm_AA_mealB_t00_rtech1_RP_short_SWATH_neg 90 1 AA 1 mealB_t00 +x091_UR_norm_MM_mealB_t02_rtech1_RP_short_SWATH_neg 91 1 MM 1 mealB_t02 +x092_UR_norm_MM_mealC_t00_rtech1_RP_short_SWATH_neg 92 1 MM 1 mealC_t00 +x093_UR_norm_MM_mealA_t04_rtech1_RP_short_SWATH_neg 93 1 MM 1 mealA_t04 +x094_UR_norm_MM_mealB_t08_rtech1_RP_short_SWATH_neg 94 1 MM 1 mealB_t08 +x095_QC_norm_17_RP_short_SWATH_neg 95 1 QC 17 QC +x096_QC_norm_18_RP_short_SWATH_neg 96 1 QC 18 QC +x097_UR_norm_DD_mealA_t07_rtech1_RP_short_SWATH_neg 97 1 DD 1 mealA_t07 +x098_UR_norm_AA_mealB_t02_rtech1_RP_short_SWATH_neg 98 1 AA 1 mealB_t02 +x099_UR_norm_AA_mealA_t02_rtech1_RP_short_SWATH_neg 99 1 AA 1 mealA_t02 +x100_UR_norm_MM_mealA_t00_rtech1_RP_short_SWATH_neg 100 1 MM 1 mealA_t00 +x101_UR_norm_DD_mealB_t01_rtech1_RP_short_SWATH_neg 101 1 DD 1 mealB_t01 +x102_UR_norm_MM_mealB_t01_rtech1_RP_short_SWATH_neg 102 1 MM 1 mealB_t01 +x103_UR_norm_AA_mealC_t06_rtech1_RP_short_SWATH_neg 103 1 AA 1 mealC_t06 +x104_UR_norm_DD_mealB_t06_rtech1_RP_short_SWATH_neg 104 1 DD 1 mealB_t06 +x105_UR_norm_DD_mealC_t08_rtech1_RP_short_SWATH_neg 105 1 DD 1 mealC_t08 +x106_UR_norm_DD_mealC_t02_rtech1_RP_short_SWATH_neg 106 1 DD 1 mealC_t02 +x107_QC_norm_19_RP_short_SWATH_neg 107 1 QC 19 QC +x108_QC_norm_20_RP_short_SWATH_neg 108 1 QC 20 QC +x109_UR_norm_DD_mealC_t06_rtech1_RP_short_SWATH_neg 109 1 DD 1 mealC_t06 +x110_UR_norm_DD_mealC_t06_rtech2_RP_short_SWATH_neg 110 1 DD 2 mealC_t06 +x111_UR_norm_MM_mealC_t05_rtech2_RP_short_SWATH_neg 111 1 MM 2 mealC_t05 +x112_UR_norm_DD_mealC_t05_rtech2_RP_short_SWATH_neg 112 1 DD 2 mealC_t05 +x113_UR_norm_DD_mealC_t00_rtech2_RP_short_SWATH_neg 113 1 DD 2 mealC_t00 +x114_UR_norm_MM_mealC_t06_rtech2_RP_short_SWATH_neg 114 1 MM 2 mealC_t06 +x115_UR_norm_AA_mealA_t00_rtech2_RP_short_SWATH_neg 115 1 AA 2 mealA_t00 +x116_UR_norm_AA_mealC_t01_rtech2_RP_short_SWATH_neg 116 1 AA 2 mealC_t01 +x117_UR_norm_DD_mealC_t02_rtech2_RP_short_SWATH_neg 117 1 DD 2 mealC_t02 +x118_UR_norm_DD_mealB_t03_rtech2_RP_short_SWATH_neg 118 1 DD 2 mealB_t03 +x119_QC_norm_21_RP_short_SWATH_neg 119 1 QC 21 QC +x120_QC_norm_22_RP_short_SWATH_neg 120 1 QC 22 QC +x121_UR_norm_MM_mealC_t08_rtech2_RP_short_SWATH_neg 121 1 MM 2 mealC_t08 +x122_UR_norm_DD_mealC_t04_rtech2_RP_short_SWATH_neg 122 1 DD 2 mealC_t04 +x123_UR_norm_DD_mealC_t08_rtech2_RP_short_SWATH_neg 123 1 DD 2 mealC_t08 +x124_UR_norm_MM_mealA_t07_rtech2_RP_short_SWATH_neg 124 1 MM 2 mealA_t07 +x125_UR_norm_AA_mealC_t05_rtech2_RP_short_SWATH_neg 125 1 AA 2 mealC_t05 +x126_UR_norm_AA_mealB_t05_rtech2_RP_short_SWATH_neg 126 1 AA 2 mealB_t05 +x127_UR_norm_MM_mealA_t06_rtech2_RP_short_SWATH_neg 127 1 MM 2 mealA_t06 +x128_UR_norm_DD_mealA_t06_rtech2_RP_short_SWATH_neg 128 1 DD 2 mealA_t06 +x129_UR_norm_AA_mealA_t03_rtech2_RP_short_SWATH_neg 129 1 AA 2 mealA_t03 +x130_UR_norm_MM_mealB_t02_rtech2_RP_short_SWATH_neg 130 1 MM 2 mealB_t02 +x131_QC_norm_23_RP_short_SWATH_neg 131 1 QC 23 QC +x132_QC_norm_24_RP_short_SWATH_neg 132 1 QC 24 QC +x133_UR_norm_DD_mealC_t07_rtech2_RP_short_SWATH_neg 133 1 DD 2 mealC_t07 +x134_UR_norm_MM_mealB_t06_rtech2_RP_short_SWATH_neg 134 1 MM 2 mealB_t06 +x135_UR_norm_DD_mealB_t08_rtech2_RP_short_SWATH_neg 135 1 DD 2 mealB_t08 +x136_UR_norm_AA_mealB_t07_rtech2_RP_short_SWATH_neg 136 1 AA 2 mealB_t07 +x137_UR_norm_MM_mealA_t00_rtech2_RP_short_SWATH_neg 137 1 MM 2 mealA_t00 +x138_UR_norm_DD_mealA_t08_rtech2_RP_short_SWATH_neg 138 1 DD 2 mealA_t08 +x139_UR_norm_AA_mealA_t08_rtech2_RP_short_SWATH_neg 139 1 AA 2 mealA_t08 +x140_UR_norm_DD_mealB_t01_rtech2_RP_short_SWATH_neg 140 1 DD 2 mealB_t01 +x141_UR_norm_AA_mealB_t08_rtech2_RP_short_SWATH_neg 141 1 AA 2 mealB_t08 +x142_UR_norm_DD_mealB_t02_rtech2_RP_short_SWATH_neg 142 1 DD 2 mealB_t02 +x143_QC_norm_25_RP_short_SWATH_neg 143 1 QC 25 QC +x144_QC_norm_26_RP_short_SWATH_neg 144 1 QC 26 QC +x145_UR_norm_DD_mealC_t01_rtech2_RP_short_SWATH_neg 145 1 DD 2 mealC_t01 +x146_UR_norm_DD_mealA_t07_rtech2_RP_short_SWATH_neg 146 1 DD 2 mealA_t07 +x147_UR_norm_DD_mealA_t00_rtech2_RP_short_SWATH_neg 147 1 DD 2 mealA_t00 +x148_UR_norm_AA_mealC_t06_rtech2_RP_short_SWATH_neg 148 1 AA 2 mealC_t06 +x149_UR_norm_MM_mealA_t05_rtech2_RP_short_SWATH_neg 149 1 MM 2 mealA_t05 +x150_UR_norm_AA_mealC_t03_rtech2_RP_short_SWATH_neg 150 1 AA 2 mealC_t03 +x151_UR_norm_DD_mealA_t01_rtech2_RP_short_SWATH_neg 151 1 DD 2 mealA_t01 +x152_UR_norm_MM_mealA_t04_rtech2_RP_short_SWATH_neg 152 1 MM 2 mealA_t04 +x153_UR_norm_MM_mealC_t01_rtech2_RP_short_SWATH_neg 153 1 MM 2 mealC_t01 +x154_UR_norm_DD_mealA_t02_rtech2_RP_short_SWATH_neg 154 1 DD 2 mealA_t02 +x155_QC_norm_27_RP_short_SWATH_neg 155 1 QC 27 QC +x156_QC_norm_28_RP_short_SWATH_neg 156 1 QC 28 QC +x157_UR_norm_MM_mealB_t03_rtech2_RP_short_SWATH_neg 157 1 MM 2 mealB_t03 +x158_UR_norm_AA_mealA_t07_rtech2_RP_short_SWATH_neg 158 1 AA 2 mealA_t07 +x159_UR_norm_MM_mealB_t04_rtech2_RP_short_SWATH_neg 159 1 MM 2 mealB_t04 +x160_UR_norm_AA_mealB_t01_rtech2_RP_short_SWATH_neg 160 1 AA 2 mealB_t01 +x161_UR_norm_MM_mealB_t00_rtech2_RP_short_SWATH_neg 161 1 MM 2 mealB_t00 +x162_UR_norm_DD_mealB_t04_rtech2_RP_short_SWATH_neg 162 1 DD 2 mealB_t04 +x163_UR_norm_MM_mealA_t03_rtech2_RP_short_SWATH_neg 163 1 MM 2 mealA_t03 +x164_UR_norm_AA_mealC_t04_rtech2_RP_short_SWATH_neg 164 1 AA 2 mealC_t04 +x165_UR_norm_AA_mealB_t06_rtech2_RP_short_SWATH_neg 165 1 AA 2 mealB_t06 +x166_UR_norm_MM_mealB_t01_rtech2_RP_short_SWATH_neg 166 1 MM 2 mealB_t01 +x167_QC_norm_29_RP_short_SWATH_neg 167 1 QC 29 QC +x168_QC_norm_30_RP_short_SWATH_neg 168 1 QC 30 QC +x169_UR_norm_DD_mealB_t06_rtech2_RP_short_SWATH_neg 169 1 DD 2 mealB_t06 +x170_UR_norm_MM_mealC_t00_rtech2_RP_short_SWATH_neg 170 1 MM 2 mealC_t00 +x171_UR_norm_AA_mealC_t07_rtech2_RP_short_SWATH_neg 171 1 AA 2 mealC_t07 +x172_UR_norm_DD_mealB_t07_rtech2_RP_short_SWATH_neg 172 1 DD 2 mealB_t07 +x173_UR_norm_MM_mealA_t01_rtech2_RP_short_SWATH_neg 173 1 MM 2 mealA_t01 +x174_UR_norm_AA_mealA_t06_rtech2_RP_short_SWATH_neg 174 1 AA 2 mealA_t06 +x175_UR_norm_MM_mealC_t02_rtech2_RP_short_SWATH_neg 175 1 MM 2 mealC_t02 +x176_UR_norm_AA_mealB_t03_rtech2_RP_short_SWATH_neg 176 1 AA 2 mealB_t03 +x177_UR_norm_MM_mealA_t08_rtech2_RP_short_SWATH_neg 177 1 MM 2 mealA_t08 +x178_UR_norm_DD_mealA_t04_rtech2_RP_short_SWATH_neg 178 1 DD 2 mealA_t04 +x179_QC_norm_31_RP_short_SWATH_neg 179 1 QC 31 QC +x180_QC_norm_32_RP_short_SWATH_neg 180 1 QC 32 QC +x181_UR_norm_AA_mealA_t04_rtech2_RP_short_SWATH_neg 181 1 AA 2 mealA_t04 +x182_UR_norm_AA_mealC_t00_rtech2_RP_short_SWATH_neg 182 1 AA 2 mealC_t00 +x183_UR_norm_AA_mealC_t08_rtech2_RP_short_SWATH_neg 183 1 AA 2 mealC_t08 +x184_UR_norm_DD_mealA_t03_rtech2_RP_short_SWATH_neg 184 1 DD 2 mealA_t03 +x185_UR_norm_AA_mealC_t02_rtech2_RP_short_SWATH_neg 185 1 AA 2 mealC_t02 +x186_UR_norm_AA_mealB_t00_rtech2_RP_short_SWATH_neg 186 1 AA 2 mealB_t00 +x187_UR_norm_MM_mealC_t04_rtech2_RP_short_SWATH_neg 187 1 MM 2 mealC_t04 +x188_UR_norm_AA_mealA_t01_rtech2_RP_short_SWATH_neg 188 1 AA 2 mealA_t01 +x189_UR_norm_MM_mealC_t03_rtech2_RP_short_SWATH_neg 189 1 MM 2 mealC_t03 +x190_UR_norm_MM_mealB_t08_rtech2_RP_short_SWATH_neg 190 1 MM 2 mealB_t08 +x191_QC_norm_33_RP_short_SWATH_neg 191 1 QC 33 QC +x192_QC_norm_34_RP_short_SWATH_neg 192 1 QC 34 QC +x193_UR_norm_MM_mealA_t02_rtech2_RP_short_SWATH_neg 193 1 MM 2 mealA_t02 +x194_UR_norm_DD_mealB_t00_rtech2_RP_short_SWATH_neg 194 1 DD 2 mealB_t00 +x195_UR_norm_MM_mealB_t05_rtech2_RP_short_SWATH_neg 195 1 MM 2 mealB_t05 +x196_UR_norm_DD_mealA_t05_rtech2_RP_short_SWATH_neg 196 1 DD 2 mealA_t05 +x197_UR_norm_AA_mealB_t02_rtech2_RP_short_SWATH_neg 197 1 AA 2 mealB_t02 +x198_UR_norm_AA_mealA_t02_rtech2_RP_short_SWATH_neg 198 1 AA 2 mealA_t02 +x199_UR_norm_MM_mealB_t07_rtech2_RP_short_SWATH_neg 199 1 MM 2 mealB_t07 +x200_UR_norm_DD_mealC_t03_rtech2_RP_short_SWATH_neg 200 1 DD 2 mealC_t03 +x201_UR_norm_AA_mealB_t04_rtech2_RP_short_SWATH_neg 201 2 AA 2 mealB_t04 +x202_UR_norm_DD_mealB_t05_rtech2_RP_short_SWATH_neg 202 2 DD 2 mealB_t05 +x203_QC_norm_35_RP_short_SWATH_neg 203 2 QC 35 QC +x204_QC_norm_36_RP_short_SWATH_neg 204 2 QC 36 QC +x205_UR_norm_MM_mealC_t07_rtech2_RP_short_SWATH_neg 205 2 MM 2 mealC_t07 +x206_UR_norm_AA_mealA_t05_rtech2_RP_short_SWATH_neg 206 2 AA 2 mealA_t05 +x207_UR_norm_AA_mealC_t07_rtech3_RP_short_SWATH_neg 207 2 AA 3 mealC_t07 +x208_UR_norm_DD_mealB_t00_rtech3_RP_short_SWATH_neg 208 2 DD 3 mealB_t00 +x209_UR_norm_MM_mealC_t04_rtech3_RP_short_SWATH_neg 209 2 MM 3 mealC_t04 +x210_UR_norm_DD_mealA_t07_rtech3_RP_short_SWATH_neg 210 2 DD 3 mealA_t07 +x211_UR_norm_MM_mealC_t00_rtech3_RP_short_SWATH_neg 211 2 MM 3 mealC_t00 +x212_UR_norm_MM_mealB_t01_rtech3_RP_short_SWATH_neg 212 2 MM 3 mealB_t01 +x213_UR_norm_AA_mealB_t02_rtech3_RP_short_SWATH_neg 213 2 AA 3 mealB_t02 +x214_QC_norm_37_RP_short_SWATH_neg 214 2 QC 37 QC +x215_QC_norm_38_RP_short_SWATH_neg 215 2 QC 38 QC +x216_UR_norm_DD_mealA_t05_rtech3_RP_short_SWATH_neg 216 2 DD 3 mealA_t05 +x217_UR_norm_DD_mealC_t03_rtech3_RP_short_SWATH_neg 217 2 DD 3 mealC_t03 +x218_UR_norm_MM_mealB_t04_rtech3_RP_short_SWATH_neg 218 2 MM 3 mealB_t04 +x219_UR_norm_DD_mealA_t03_rtech3_RP_short_SWATH_neg 219 2 DD 3 mealA_t03 +x220_UR_norm_AA_mealB_t00_rtech3_RP_short_SWATH_neg 220 2 AA 3 mealB_t00 +x221_UR_norm_MM_mealB_t08_rtech3_RP_short_SWATH_neg 221 2 MM 3 mealB_t08 +x222_UR_norm_DD_mealC_t01_rtech3_RP_short_SWATH_neg 222 2 DD 3 mealC_t01 +x223_UR_norm_DD_mealA_t02_rtech3_RP_short_SWATH_neg 223 2 DD 3 mealA_t02 +x224_UR_norm_AA_mealB_t06_rtech3_RP_short_SWATH_neg 224 2 AA 3 mealB_t06 +x225_UR_norm_MM_mealA_t07_rtech3_RP_short_SWATH_neg 225 2 MM 3 mealA_t07 +x226_QC_norm_39_RP_short_SWATH_neg 226 2 QC 39 QC +x227_QC_norm_40_RP_short_SWATH_neg 227 2 QC 40 QC +x228_UR_norm_AA_mealA_t00_rtech3_RP_short_SWATH_neg 228 2 AA 3 mealA_t00 +x229_UR_norm_DD_mealA_t04_rtech3_RP_short_SWATH_neg 229 2 DD 3 mealA_t04 +x230_UR_norm_DD_mealB_t07_rtech3_RP_short_SWATH_neg 230 2 DD 3 mealB_t07 +x231_UR_norm_MM_mealA_t01_rtech3_RP_short_SWATH_neg 231 2 MM 3 mealA_t01 +x232_UR_norm_DD_mealB_t01_rtech3_RP_short_SWATH_neg 232 2 DD 3 mealB_t01 +x233_UR_norm_AA_mealA_t01_rtech3_RP_short_SWATH_neg 233 2 AA 3 mealA_t01 +x234_UR_norm_AA_mealA_t05_rtech3_RP_short_SWATH_neg 234 2 AA 3 mealA_t05 +x235_UR_norm_MM_mealA_t03_rtech3_RP_short_SWATH_neg 235 2 MM 3 mealA_t03 +x236_UR_norm_DD_mealC_t07_rtech3_RP_short_SWATH_neg 236 2 DD 3 mealC_t07 +x237_UR_norm_MM_mealC_t07_rtech3_RP_short_SWATH_neg 237 2 MM 3 mealC_t07 +x238_QC_norm_41_RP_short_SWATH_neg 238 2 QC 41 QC +x239_QC_norm_42_RP_short_SWATH_neg 239 2 QC 42 QC +x240_UR_norm_MM_mealA_t05_rtech3_RP_short_SWATH_neg 240 2 MM 3 mealA_t05 +x241_UR_norm_AA_mealA_t08_rtech3_RP_short_SWATH_neg 241 2 AA 3 mealA_t08 +x242_UR_norm_MM_mealB_t00_rtech3_RP_short_SWATH_neg 242 2 MM 3 mealB_t00 +x243_UR_norm_DD_mealC_t08_rtech3_RP_short_SWATH_neg 243 2 DD 3 mealC_t08 +x244_UR_norm_AA_mealB_t08_rtech3_RP_short_SWATH_neg 244 2 AA 3 mealB_t08 +x245_UR_norm_MM_mealC_t02_rtech3_RP_short_SWATH_neg 245 2 MM 3 mealC_t02 +x246_UR_norm_AA_mealB_t03_rtech3_RP_short_SWATH_neg 246 2 AA 3 mealB_t03 +x247_UR_norm_DD_mealC_t02_rtech3_RP_short_SWATH_neg 247 2 DD 3 mealC_t02 +x248_UR_norm_DD_mealC_t05_rtech3_RP_short_SWATH_neg 248 2 DD 3 mealC_t05 +x249_UR_norm_DD_mealC_t04_rtech3_RP_short_SWATH_neg 249 2 DD 3 mealC_t04 +x250_QC_norm_43_RP_short_SWATH_neg 250 2 QC 43 QC +x251_QC_norm_44_RP_short_SWATH_neg 251 2 QC 44 QC +x252_UR_norm_MM_mealC_t03_rtech3_RP_short_SWATH_neg 252 2 MM 3 mealC_t03 +x253_UR_norm_DD_mealB_t08_rtech3_RP_short_SWATH_neg 253 2 DD 3 mealB_t08 +x254_UR_norm_DD_mealA_t01_rtech3_RP_short_SWATH_neg 254 2 DD 3 mealA_t01 +x255_UR_norm_MM_mealC_t06_rtech3_RP_short_SWATH_neg 255 2 MM 3 mealC_t06 +x256_UR_norm_MM_mealB_t03_rtech3_RP_short_SWATH_neg 256 2 MM 3 mealB_t03 +x257_UR_norm_AA_mealC_t01_rtech3_RP_short_SWATH_neg 257 2 AA 3 mealC_t01 +x258_UR_norm_DD_mealB_t04_rtech3_RP_short_SWATH_neg 258 2 DD 3 mealB_t04 +x259_UR_norm_AA_mealC_t08_rtech3_RP_short_SWATH_neg 259 2 AA 3 mealC_t08 +x260_UR_norm_MM_mealA_t00_rtech3_RP_short_SWATH_neg 260 2 MM 3 mealA_t00 +x261_UR_norm_DD_mealB_t02_rtech3_RP_short_SWATH_neg 261 2 DD 3 mealB_t02 +x262_QC_norm_45_RP_short_SWATH_neg 262 2 QC 45 QC +x263_QC_norm_46_RP_short_SWATH_neg 263 2 QC 46 QC +x264_UR_norm_MM_mealA_t04_rtech3_RP_short_SWATH_neg 264 2 MM 3 mealA_t04 +x265_UR_norm_MM_mealB_t05_rtech3_RP_short_SWATH_neg 265 2 MM 3 mealB_t05 +x266_UR_norm_MM_mealA_t02_rtech3_RP_short_SWATH_neg 266 2 MM 3 mealA_t02 +x267_UR_norm_DD_mealA_t00_rtech3_RP_short_SWATH_neg 267 2 DD 3 mealA_t00 +x268_UR_norm_AA_mealB_t04_rtech3_RP_short_SWATH_neg 268 2 AA 3 mealB_t04 +x269_UR_norm_DD_mealC_t06_rtech3_RP_short_SWATH_neg 269 2 DD 3 mealC_t06 +x270_UR_norm_DD_mealB_t06_rtech3_RP_short_SWATH_neg 270 2 DD 3 mealB_t06 +x271_UR_norm_AA_mealC_t06_rtech3_RP_short_SWATH_neg 271 2 AA 3 mealC_t06 +x272_UR_norm_AA_mealA_t04_rtech3_RP_short_SWATH_neg 272 2 AA 3 mealA_t04 +x273_UR_norm_MM_mealA_t08_rtech3_RP_short_SWATH_neg 273 2 MM 3 mealA_t08 +x274_QC_norm_47_RP_short_SWATH_neg 274 2 QC 47 QC +x275_QC_norm_48_RP_short_SWATH_neg 275 2 QC 48 QC +x276_UR_norm_MM_mealB_t07_rtech3_RP_short_SWATH_neg 276 2 MM 3 mealB_t07 +x277_UR_norm_AA_mealB_t01_rtech3_RP_short_SWATH_neg 277 2 AA 3 mealB_t01 +x278_UR_norm_AA_mealC_t03_rtech3_RP_short_SWATH_neg 278 2 AA 3 mealC_t03 +x279_UR_norm_DD_mealB_t03_rtech3_RP_short_SWATH_neg 279 2 DD 3 mealB_t03 +x280_UR_norm_MM_mealB_t06_rtech3_RP_short_SWATH_neg 280 2 MM 3 mealB_t06 +x281_UR_norm_MM_mealB_t02_rtech3_RP_short_SWATH_neg 281 2 MM 3 mealB_t02 +x282_UR_norm_MM_mealA_t06_rtech3_RP_short_SWATH_neg 282 2 MM 3 mealA_t06 +x283_UR_norm_DD_mealB_t05_rtech3_RP_short_SWATH_neg 283 2 DD 3 mealB_t05 +x284_UR_norm_AA_mealA_t03_rtech3_RP_short_SWATH_neg 284 2 AA 3 mealA_t03 +x285_UR_norm_DD_mealC_t00_rtech3_RP_short_SWATH_neg 285 2 DD 3 mealC_t00 +x286_QC_norm_49_RP_short_SWATH_neg 286 2 QC 49 QC +x287_QC_norm_50_RP_short_SWATH_neg 287 2 QC 50 QC +x288_UR_norm_AA_mealB_t07_rtech3_RP_short_SWATH_neg 288 2 AA 3 mealB_t07 +x289_UR_norm_AA_mealB_t05_rtech3_RP_short_SWATH_neg 289 2 AA 3 mealB_t05 +x290_UR_norm_AA_mealC_t02_rtech3_RP_short_SWATH_neg 290 2 AA 3 mealC_t02 +x291_UR_norm_DD_mealA_t08_rtech3_RP_short_SWATH_neg 291 2 DD 3 mealA_t08 +x292_UR_norm_MM_mealC_t08_rtech3_RP_short_SWATH_neg 292 2 MM 3 mealC_t08 +x293_UR_norm_DD_mealA_t06_rtech3_RP_short_SWATH_neg 293 2 DD 3 mealA_t06 +x294_UR_norm_AA_mealA_t07_rtech3_RP_short_SWATH_neg 294 2 AA 3 mealA_t07 +x295_QC_norm_51_RP_short_SWATH_neg 295 2 QC 51 QC +x296_QC_norm_52_RP_short_SWATH_neg 296 2 QC 52 QC +x297_UR_norm_AA_mealA_t06_rtech3_RP_short_SWATH_neg 297 2 AA 3 mealA_t06 +x298_UR_norm_AA_mealA_t02_rtech3_RP_short_SWATH_neg 298 2 AA 3 mealA_t02 +x299_UR_norm_AA_mealC_t00_rtech3_RP_short_SWATH_neg 299 2 AA 3 mealC_t00 +x300_UR_norm_MM_mealC_t01_rtech3_RP_short_SWATH_neg 300 2 MM 3 mealC_t01 +x301_UR_norm_AA_mealC_t05_rtech3_RP_short_SWATH_neg 301 2 AA 3 mealC_t05 +x302_UR_norm_AA_mealC_t04_rtech3_RP_short_SWATH_neg 302 2 AA 3 mealC_t04 +x303_UR_norm_MM_mealC_t05_rtech3_RP_short_SWATH_neg 303 2 MM 3 mealC_t05 +x304_QC_norm_53_RP_short_SWATH_neg 304 2 QC 53 QC +x305_QC_norm_54_RP_short_SWATH_neg 305 2 QC 54 QC +x306_BananaShake_norm_rtech1_RP_short_SWATH_neg 306 2 meal A 1 A +x307_PapayaShake_norm_rtech1_RP_short_SWATH_neg 307 2 meal B 1 B +x308_KefirShake_norm_rtech1_RP_short_SWATH_neg 308 2 meal C 1 C +x309_QC_norm_55_RP_short_SWATH_neg 309 2 QC 55 QC +x310_KefirShake_norm_rtech2_RP_short_SWATH_neg 310 2 meal C 2 C +x311_PapayaShake_norm_rtech2_RP_short_SWATH_neg 311 2 meal B 2 B +x312_BananaShake_norm_rtech2_RP_short_SWATH_neg 312 2 meal A 2 A +x313_QC_norm_56_RP_short_SWATH_neg 313 2 QC 56 QC +x314_PapayaShake_norm_rtech3_RP_short_SWATH_neg 314 2 meal B 3 B +x315_BananaShake_norm_rtech3_RP_short_SWATH_neg 315 2 meal A 3 A +x316_KefirShake_norm_rtech3_RP_short_SWATH_neg 316 2 meal C 3 C \ No newline at end of file diff --git a/inst/extdata/Urine_RP_POS_norm_metadata.txt b/inst/extdata/Urine_RP_POS_norm_metadata.txt new file mode 100644 index 0000000..0c04394 --- /dev/null +++ b/inst/extdata/Urine_RP_POS_norm_metadata.txt @@ -0,0 +1,317 @@ +id injection_order batch class technical_rep biological_rep +x001_Blank_1_norm_RP_short_SWATH_pos 1 1 Blank 1 Blank +x002_Blank_1_norm_RP_short_SWATH_pos 2 1 Blank 1 Blank +x003_Blank_1_norm_RP_short_SWATH_pos 3 1 Blank 1 Blank +x004_QC_norm_equil_01_RP_short_SWATH_pos 4 1 QC 1 QC_equil_1 +x005_QC_norm_equil_02_RP_short_SWATH_pos 5 1 QC 2 QC_equil_2 +x006_QC_norm_equil_03_RP_short_SWATH_pos 6 1 QC 3 QC_equil_3 +x007_QC_norm_equil_04_RP_short_SWATH_pos 7 1 QC 4 QC_equil_4 +x008_QC_norm_equil_05_RP_short_SWATH_pos 8 1 QC 5 QC_equil_5 +x009_QC_norm_01_RP_short_SWATH_pos 9 1 QC 1 QC +x010_QC_norm_02_RP_short_SWATH_pos 10 1 QC 2 QC +x011_QC_norm_03_RP_short_SWATH_pos 11 1 QC 3 QC +x012_QC_norm_04_RP_short_SWATH_pos 12 1 QC 4 QC +x013_QC_norm_05_RP_short_SWATH_pos 13 1 QC 5 QC +x014_UR_norm_DD_mealC_t07_rtech1_RP_short_SWATH_pos 14 1 DD 1 mealC_t07 +x015_UR_norm_MM_mealB_t00_rtech1_RP_short_SWATH_pos 15 1 MM 1 mealB_t00 +x016_UR_norm_AA_mealA_t00_rtech1_RP_short_SWATH_pos 16 1 AA 1 mealA_t00 +x017_UR_norm_AA_mealC_t01_rtech1_RP_short_SWATH_pos 17 1 AA 1 mealC_t01 +x018_UR_norm_DD_mealA_t06_rtech1_RP_short_SWATH_pos 18 1 DD 1 mealA_t06 +x019_UR_norm_MM_mealC_t08_rtech1_RP_short_SWATH_pos 19 1 MM 1 mealC_t08 +x020_UR_norm_DD_mealA_t01_rtech1_RP_short_SWATH_pos 20 1 DD 1 mealA_t01 +x021_UR_norm_AA_mealC_t02_rtech1_RP_short_SWATH_pos 21 1 AA 1 mealC_t02 +x022_UR_norm_DD_mealA_t05_rtech1_RP_short_SWATH_pos 22 1 DD 1 mealA_t05 +x023_UR_norm_DD_mealC_t00_rtech1_RP_short_SWATH_pos 23 1 DD 1 mealC_t00 +x024_QC_norm_06_RP_short_SWATH_pos 24 1 QC 6 QC +x025_QC_norm_07_RP_short_SWATH_pos 25 1 QC 7 QC +x026_UR_norm_MM_mealA_t08_rtech1_RP_short_SWATH_pos 26 1 MM 1 mealA_t08 +x027_UR_norm_DD_mealB_t08_rtech1_RP_short_SWATH_pos 27 1 DD 1 mealB_t08 +x028_UR_norm_MM_mealA_t01_rtech1_RP_short_SWATH_pos 28 1 MM 1 mealA_t01 +x029_UR_norm_AA_mealA_t01_rtech1_RP_short_SWATH_pos 29 1 AA 1 mealA_t01 +x030_UR_norm_AA_mealB_t04_rtech1_RP_short_SWATH_pos 30 1 AA 1 mealB_t04 +x031_UR_norm_AA_mealB_t03_rtech1_RP_short_SWATH_pos 31 1 AA 1 mealB_t03 +x032_UR_norm_DD_mealC_t05_rtech1_RP_short_SWATH_pos 32 1 DD 1 mealC_t05 +x033_UR_norm_AA_mealC_t00_rtech1_RP_short_SWATH_pos 33 1 AA 1 mealC_t00 +x034_UR_norm_MM_mealB_t07_rtech1_RP_short_SWATH_pos 34 1 MM 1 mealB_t07 +x035_UR_norm_MM_mealA_t02_rtech1_RP_short_SWATH_pos 35 1 MM 1 mealA_t02 +x036_QC_norm_08_RP_short_SWATH_pos 36 1 QC 8 QC +x037_QC_norm_09_RP_short_SWATH_pos 37 1 QC 9 QC +x038_UR_norm_DD_mealC_t01_rtech1_RP_short_SWATH_pos 38 1 DD 1 mealC_t01 +x039_UR_norm_DD_mealA_t00_rtech1_RP_short_SWATH_pos 39 1 DD 1 mealA_t00 +x040_UR_norm_DD_mealA_t03_rtech1_RP_short_SWATH_pos 40 1 DD 1 mealA_t03 +x041_UR_norm_DD_mealC_t03_rtech1_RP_short_SWATH_pos 41 1 DD 1 mealC_t03 +x042_UR_norm_AA_mealA_t04_rtech1_RP_short_SWATH_pos 42 1 AA 1 mealA_t04 +x043_UR_norm_AA_mealB_t08_rtech1_RP_short_SWATH_pos 43 1 AA 1 mealB_t08 +x044_UR_norm_AA_mealB_t01_rtech1_RP_short_SWATH_pos 44 1 AA 1 mealB_t01 +x045_UR_norm_AA_mealB_t05_rtech1_RP_short_SWATH_pos 45 1 AA 1 mealB_t05 +x046_UR_norm_MM_mealC_t04_rtech1_RP_short_SWATH_pos 46 1 MM 1 mealC_t04 +x047_UR_norm_MM_mealC_t02_rtech1_RP_short_SWATH_pos 47 1 MM 1 mealC_t02 +x048_QC_norm_10_RP_short_SWATH_pos 48 1 QC 10 QC +x049_QC_norm_11_RP_short_SWATH_pos 49 1 QC 11 QC +x050_UR_norm_MM_mealA_t07_rtech1_RP_short_SWATH_pos 50 1 MM 1 mealA_t07 +x051_UR_norm_DD_mealB_t02_rtech1_RP_short_SWATH_pos 51 1 DD 1 mealB_t02 +x052_UR_norm_MM_mealC_t07_rtech1_RP_short_SWATH_pos 52 1 MM 1 mealC_t07 +x053_UR_norm_DD_mealB_t07_rtech1_RP_short_SWATH_pos 53 1 DD 1 mealB_t07 +x054_UR_norm_MM_mealC_t01_rtech1_RP_short_SWATH_pos 54 1 MM 1 mealC_t01 +x055_UR_norm_DD_mealA_t04_rtech1_RP_short_SWATH_pos 55 1 DD 1 mealA_t04 +x056_UR_norm_MM_mealB_t05_rtech1_RP_short_SWATH_pos 56 1 MM 1 mealB_t05 +x057_UR_norm_DD_mealB_t05_rtech1_RP_short_SWATH_pos 57 1 DD 1 mealB_t05 +x058_UR_norm_AA_mealA_t07_rtech1_RP_short_SWATH_pos 58 1 AA 1 mealA_t07 +x059_UR_norm_AA_mealA_t05_rtech1_RP_short_SWATH_pos 59 1 AA 1 mealA_t05 +x060_QC_norm_12_RP_short_SWATH_pos 60 1 QC 12 QC +x061_UR_norm_MM_mealB_t04_rtech1_RP_short_SWATH_pos 61 1 MM 1 mealB_t04 +x062_UR_norm_MM_mealB_t06_rtech1_RP_short_SWATH_pos 62 1 MM 1 mealB_t06 +x063_UR_norm_AA_mealB_t07_rtech1_RP_short_SWATH_pos 63 1 AA 1 mealB_t07 +x064_UR_norm_MM_mealC_t03_rtech1_RP_short_SWATH_pos 64 1 MM 1 mealC_t03 +x065_UR_norm_MM_mealC_t05_rtech1_RP_short_SWATH_pos 65 1 MM 1 mealC_t05 +x066_UR_norm_MM_mealA_t03_rtech1_RP_short_SWATH_pos 66 1 MM 1 mealA_t03 +x067_UR_norm_DD_mealB_t04_rtech1_RP_short_SWATH_pos 67 1 DD 1 mealB_t04 +x068_UR_norm_AA_mealC_t07_rtech1_RP_short_SWATH_pos 68 1 AA 1 mealC_t07 +x069_UR_norm_AA_mealC_t05_rtech1_RP_short_SWATH_pos 69 1 AA 1 mealC_t05 +x070_UR_norm_MM_mealA_t05_rtech1_RP_short_SWATH_pos 70 1 MM 1 mealA_t05 +x071_QC_norm_13_RP_short_SWATH_pos 71 1 QC 13 QC +x072_QC_norm_14_RP_short_SWATH_pos 72 1 QC 14 QC +x073_UR_norm_MM_mealB_t03_rtech1_RP_short_SWATH_pos 73 1 MM 1 mealB_t03 +x074_UR_norm_DD_mealB_t00_rtech1_RP_short_SWATH_pos 74 1 DD 1 mealB_t00 +x075_UR_norm_MM_mealC_t06_rtech1_RP_short_SWATH_pos 75 1 MM 1 mealC_t06 +x076_UR_norm_AA_mealA_t06_rtech1_RP_short_SWATH_pos 76 1 AA 1 mealA_t06 +x077_UR_norm_DD_mealC_t04_rtech1_RP_short_SWATH_pos 77 1 DD 1 mealC_t04 +x078_UR_norm_AA_mealB_t06_rtech1_RP_short_SWATH_pos 78 1 AA 1 mealB_t06 +x079_UR_norm_DD_mealA_t02_rtech1_RP_short_SWATH_pos 79 1 DD 1 mealA_t02 +x080_UR_norm_DD_mealB_t03_rtech1_RP_short_SWATH_pos 80 1 DD 1 mealB_t03 +x081_UR_norm_AA_mealA_t08_rtech1_RP_short_SWATH_pos 81 1 AA 1 mealA_t08 +x082_UR_norm_AA_mealC_t04_rtech1_RP_short_SWATH_pos 82 1 AA 1 mealC_t04 +x083_QC_norm_15_RP_short_SWATH_pos 83 1 QC 15 QC +x084_QC_norm_16_RP_short_SWATH_pos 84 1 QC 16 QC +x085_UR_norm_AA_mealC_t08_rtech1_RP_short_SWATH_pos 85 1 AA 1 mealC_t08 +x086_UR_norm_MM_mealA_t06_rtech1_RP_short_SWATH_pos 86 1 MM 1 mealA_t06 +x087_UR_norm_AA_mealA_t03_rtech1_RP_short_SWATH_pos 87 1 AA 1 mealA_t03 +x088_UR_norm_AA_mealC_t03_rtech1_RP_short_SWATH_pos 88 1 AA 1 mealC_t03 +x089_UR_norm_DD_mealA_t08_rtech1_RP_short_SWATH_pos 89 1 DD 1 mealA_t08 +x090_UR_norm_AA_mealB_t00_rtech1_RP_short_SWATH_pos 90 1 AA 1 mealB_t00 +x091_UR_norm_MM_mealB_t02_rtech1_RP_short_SWATH_pos 91 1 MM 1 mealB_t02 +x092_UR_norm_MM_mealC_t00_rtech1_RP_short_SWATH_pos 92 1 MM 1 mealC_t00 +x093_UR_norm_MM_mealA_t04_rtech1_RP_short_SWATH_pos 93 1 MM 1 mealA_t04 +x094_UR_norm_MM_mealB_t08_rtech1_RP_short_SWATH_pos 94 1 MM 1 mealB_t08 +x095_QC_norm_17_RP_short_SWATH_pos 95 1 QC 17 QC +x096_QC_norm_18_RP_short_SWATH_pos 96 1 QC 18 QC +x097_UR_norm_DD_mealA_t07_rtech1_RP_short_SWATH_pos 97 1 DD 1 mealA_t07 +x098_UR_norm_AA_mealB_t02_rtech1_RP_short_SWATH_pos 98 1 AA 1 mealB_t02 +x099_UR_norm_AA_mealA_t02_rtech1_RP_short_SWATH_pos 99 1 AA 1 mealA_t02 +x100_UR_norm_MM_mealA_t00_rtech1_RP_short_SWATH_pos 100 1 MM 1 mealA_t00 +x101_UR_norm_DD_mealB_t01_rtech1_RP_short_SWATH_pos 101 1 DD 1 mealB_t01 +x102_UR_norm_MM_mealB_t01_rtech1_RP_short_SWATH_pos 102 1 MM 1 mealB_t01 +x103_UR_norm_AA_mealC_t06_rtech1_RP_short_SWATH_pos 103 1 AA 1 mealC_t06 +x104_UR_norm_DD_mealB_t06_rtech1_RP_short_SWATH_pos 104 1 DD 1 mealB_t06 +x105_UR_norm_DD_mealC_t08_rtech1_RP_short_SWATH_pos 105 1 DD 1 mealC_t08 +x106_UR_norm_DD_mealC_t02_rtech1_RP_short_SWATH_pos 106 1 DD 1 mealC_t02 +x107_QC_norm_19_RP_short_SWATH_pos 107 1 QC 19 QC +x108_QC_norm_20_RP_short_SWATH_pos 108 1 QC 20 QC +x109_UR_norm_DD_mealC_t06_rtech1_RP_short_SWATH_pos 109 1 DD 1 mealC_t06 +x110_UR_norm_DD_mealC_t06_rtech2_RP_short_SWATH_pos 110 1 DD 2 mealC_t06 +x111_UR_norm_MM_mealC_t05_rtech2_RP_short_SWATH_pos 111 1 MM 2 mealC_t05 +x112_UR_norm_DD_mealC_t05_rtech2_RP_short_SWATH_pos 112 1 DD 2 mealC_t05 +x113_UR_norm_DD_mealC_t00_rtech2_RP_short_SWATH_pos 113 1 DD 2 mealC_t00 +x114_UR_norm_MM_mealC_t06_rtech2_RP_short_SWATH_pos 114 1 MM 2 mealC_t06 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2 AA 3 mealA_t00 +x229_UR_norm_DD_mealA_t04_rtech3_RP_short_SWATH_pos 229 2 DD 3 mealA_t04 +x230_UR_norm_DD_mealB_t07_rtech3_RP_short_SWATH_pos 230 2 DD 3 mealB_t07 +x231_UR_norm_MM_mealA_t01_rtech3_RP_short_SWATH_pos 231 2 MM 3 mealA_t01 +x232_UR_norm_DD_mealB_t01_rtech3_RP_short_SWATH_pos 232 2 DD 3 mealB_t01 +x233_UR_norm_AA_mealA_t01_rtech3_RP_short_SWATH_pos 233 2 AA 3 mealA_t01 +x234_UR_norm_AA_mealA_t05_rtech3_RP_short_SWATH_pos 234 2 AA 3 mealA_t05 +x235_UR_norm_MM_mealA_t03_rtech3_RP_short_SWATH_pos 235 2 MM 3 mealA_t03 +x236_UR_norm_DD_mealC_t07_rtech3_RP_short_SWATH_pos 236 2 DD 3 mealC_t07 +x237_UR_norm_MM_mealC_t07_rtech3_RP_short_SWATH_pos 237 2 MM 3 mealC_t07 +x238_QC_norm_41_RP_short_SWATH_pos 238 2 QC 41 QC +x239_QC_norm_42_RP_short_SWATH_pos 239 2 QC 42 QC +x240_UR_norm_MM_mealA_t05_rtech3_RP_short_SWATH_pos 240 2 MM 3 mealA_t05 +x241_UR_norm_AA_mealA_t08_rtech3_RP_short_SWATH_pos 241 2 AA 3 mealA_t08 +x242_UR_norm_MM_mealB_t00_rtech3_RP_short_SWATH_pos 242 2 MM 3 mealB_t00 +x243_UR_norm_DD_mealC_t08_rtech3_RP_short_SWATH_pos 243 2 DD 3 mealC_t08 +x244_UR_norm_AA_mealB_t08_rtech3_RP_short_SWATH_pos 244 2 AA 3 mealB_t08 +x245_UR_norm_MM_mealC_t02_rtech3_RP_short_SWATH_pos 245 2 MM 3 mealC_t02 +x246_UR_norm_AA_mealB_t03_rtech3_RP_short_SWATH_pos 246 2 AA 3 mealB_t03 +x247_UR_norm_DD_mealC_t02_rtech3_RP_short_SWATH_pos 247 2 DD 3 mealC_t02 +x248_UR_norm_DD_mealC_t05_rtech3_RP_short_SWATH_pos 248 2 DD 3 mealC_t05 +x249_UR_norm_DD_mealC_t04_rtech3_RP_short_SWATH_pos 249 2 DD 3 mealC_t04 +x250_QC_norm_43_RP_short_SWATH_pos 250 2 QC 43 QC +x251_QC_norm_44_RP_short_SWATH_pos 251 2 QC 44 QC +x252_UR_norm_MM_mealC_t03_rtech3_RP_short_SWATH_pos 252 2 MM 3 mealC_t03 +x253_UR_norm_DD_mealB_t08_rtech3_RP_short_SWATH_pos 253 2 DD 3 mealB_t08 +x254_UR_norm_DD_mealA_t01_rtech3_RP_short_SWATH_pos 254 2 DD 3 mealA_t01 +x255_UR_norm_MM_mealC_t06_rtech3_RP_short_SWATH_pos 255 2 MM 3 mealC_t06 +x256_UR_norm_MM_mealB_t03_rtech3_RP_short_SWATH_pos 256 2 MM 3 mealB_t03 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+x285_UR_norm_DD_mealC_t00_rtech3_RP_short_SWATH_pos 285 2 DD 3 mealC_t00 +x286_QC_norm_49_RP_short_SWATH_pos 286 2 QC 49 QC +x287_QC_norm_50_RP_short_SWATH_pos 287 2 QC 50 QC +x288_UR_norm_AA_mealB_t07_rtech3_RP_short_SWATH_pos 288 2 AA 3 mealB_t07 +x289_UR_norm_AA_mealB_t05_rtech3_RP_short_SWATH_pos 289 2 AA 3 mealB_t05 +x290_UR_norm_AA_mealC_t02_rtech3_RP_short_SWATH_pos 290 2 AA 3 mealC_t02 +x291_UR_norm_DD_mealA_t08_rtech3_RP_short_SWATH_pos 291 2 DD 3 mealA_t08 +x292_UR_norm_MM_mealC_t08_rtech3_RP_short_SWATH_pos 292 2 MM 3 mealC_t08 +x293_UR_norm_DD_mealA_t06_rtech3_RP_short_SWATH_pos 293 2 DD 3 mealA_t06 +x294_UR_norm_AA_mealA_t07_rtech3_RP_short_SWATH_pos 294 2 AA 3 mealA_t07 +x295_QC_norm_51_RP_short_SWATH_pos 295 2 QC 51 QC +x296_QC_norm_52_RP_short_SWATH_pos 296 2 QC 52 QC +x297_UR_norm_AA_mealA_t06_rtech3_RP_short_SWATH_pos 297 2 AA 3 mealA_t06 +x298_UR_norm_AA_mealA_t02_rtech3_RP_short_SWATH_pos 298 2 AA 3 mealA_t02 +x299_UR_norm_AA_mealC_t00_rtech3_RP_short_SWATH_pos 299 2 AA 3 mealC_t00 +x300_UR_norm_MM_mealC_t01_rtech3_RP_short_SWATH_pos 300 2 MM 3 mealC_t01 +x301_UR_norm_AA_mealC_t05_rtech3_RP_short_SWATH_pos 301 2 AA 3 mealC_t05 +x302_UR_norm_AA_mealC_t04_rtech3_RP_short_SWATH_pos 302 2 AA 3 mealC_t04 +x303_UR_norm_MM_mealC_t05_rtech3_RP_short_SWATH_pos 303 2 MM 3 mealC_t05 +x304_QC_norm_53_RP_short_SWATH_pos 304 2 QC 53 QC +x305_QC_norm_54_RP_short_SWATH_pos 305 2 QC 54 QC +x306_BananaShake_norm_rtech1_RP_short_SWATH_pos 306 2 meal A 1 A +x307_PapayaShake_norm_rtech1_RP_short_SWATH_pos 307 2 meal B 1 B +x308_KefirShake_norm_rtech1_RP_short_SWATH_pos 308 2 meal C 1 C +x309_QC_norm_55_RP_short_SWATH_pos 309 2 QC 55 QC +x310_KefirShake_norm_rtech2_RP_short_SWATH_pos 310 2 meal C 2 C +x311_PapayaShake_norm_rtech2_RP_short_SWATH_pos 311 2 meal B 2 B +x312_BananaShake_norm_rtech2_RP_short_SWATH_pos 312 2 meal A 2 A +x313_QC_norm_56_RP_short_SWATH_pos 313 2 QC 56 QC +x314_PapayaShake_norm_rtech3_RP_short_SWATH_pos 314 2 meal B 3 B +x315_BananaShake_norm_rtech3_RP_short_SWATH_pos 315 2 meal A 3 A +x316_KefirShake_norm_rtech3_RP_short_SWATH_pos 316 2 meal C 3 C diff --git a/vignettes/margheRita.Rmd b/vignettes/margheRita.Rmd index 8d0670d..cc1db86 100644 --- a/vignettes/margheRita.Rmd +++ b/vignettes/margheRita.Rmd @@ -35,6 +35,11 @@ The package provides: - simplified execution of parametric and non-parametric statistical tests over a large number of features; - pathway analysis based on ORA and MSEA over various databases. +Source code: https://github.com/emosca-cnr/margheRita + +Citation: Ettore Mosca, Marynka Ulaszewska, Zahrasadat Alavikakhki, Edoardo Niccolò Bellini, Valeria Mannella, Gianfranco Frigerio, Denise Drago, Annapaola Andolfo. MargheRita: an R package for LC-MS/MS SWATH metabolomics data analysis and confident metabolite identification based on a spectral library of reference standards. bioRxiv 2024.06.20.599545; doi: https://doi.org/10.1101/2024.06.20.599545 + + Contacts: - [Annapaola Andolfo](https://research.hsr.it/en/core-facilities/promefa/annapaola-andolfo.html), Proteomics and Metabolomics Facility, HSR @@ -42,7 +47,7 @@ Contacts: # Installation -The package requires a series of other R packages, which are availble in [CRAN](https://cran.r-project.org/), [Bioconductor](https://www.bioconductor.org/) or [github](https://github.com/), namely: +The package requires a series of other R packages, which are available in [CRAN](https://cran.r-project.org/), [Bioconductor](https://www.bioconductor.org/) or [github](https://github.com/), namely: ```{r, echo=FALSE} cat(packageDescription("margheRita")$Imports) @@ -101,6 +106,13 @@ head(mL_demo$raw$QC[, 1:3]) head(mL_demo$raw$QC_ann) ``` +The full version of the "Urine" dataset, which was used for margheRita assessment and to generate this documentation, is available at https://doi.org/10.5281/zenodo.11243781, files "Urine_RP_NEG_norm.txt" and "Urine_RP_POS_norm.txt". The corresponding sample information files can be accessed as follows: + +```{r, eval=FALSE} +sample_file_NEG <- system.file("extdata", "Urine_RP_NEG_norm_metadata.txt", package = "margheRita") +sample_file_POS <- system.file("extdata", "Urine_RP_POS_norm_metadata.txt", package = "margheRita") +``` + # Inter-operability To support interoperability with other packages with a focus on metabolomics, the margheRitaList can be reorganized as a "MetaboSet" object, used by package "notame" [@Klavus2020]: