diff --git a/NAMESPACE b/NAMESPACE
index defb8da..06b68f6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,18 +1,18 @@
-# Generated by roxygen2: do not edit by hand
-
-export("%<>%")
-export("%>%")
-export(create_term_match_table)
-export(files_in_group)
-export(flatten_json)
-export(generate_json)
-export(gradient_tables)
-export(group_count)
-export(instrument_names)
-export(match_terms)
-export(one_gradient_table)
-export(one_group_match_terms)
-export(save_all_groups)
-export(save_group_table)
-importFrom(magrittr,"%<>%")
-importFrom(magrittr,"%>%")
+# Generated by roxygen2: do not edit by hand
+
+export("%<>%")
+export("%>%")
+export(create_term_match_table)
+export(files_in_group)
+export(flatten_json)
+export(generate_json)
+export(gradient_tables)
+export(group_count)
+export(instrument_names)
+export(match_terms)
+export(one_gradient_table)
+export(one_group_match_terms)
+export(save_all_groups)
+export(save_group_table)
+importFrom(magrittr,"%<>%")
+importFrom(magrittr,"%>%")
diff --git a/man/create_term_match_table.Rd b/man/create_term_match_table.Rd
index 45bd83d..80037d2 100644
--- a/man/create_term_match_table.Rd
+++ b/man/create_term_match_table.Rd
@@ -1,29 +1,29 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/load_term_matching_table_function.R
-\name{create_term_match_table}
-\alias{create_term_match_table}
-\title{create term matching Table}
-\usage{
-create_term_match_table(instrument_list = c("Thermo_EASY-nLC",
-  "Q Exactive_Plus_-_Orbitrap_MS"), origin_key = "")
-}
-\arguments{
-\item{instrument_list}{list of instruments in the raw file, get it with "instrument_names()".}
-
-\item{origin_key}{Specifies which information is required.
-If empty, all information is used.
-"jpr_guidelines_ms" for the requirements of the Journal of Proteome Research.
-"miape" for The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.}
-}
-\value{
-A table needed to extract the meta data with match_terms().
-}
-\description{
-create term matching Table
-}
-\examples{
-term_matching_table <- create_term_match_table(
-  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
-  origin_key = "jpr_guidelines_ms")
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load_term_matching_table_function.R
+\name{create_term_match_table}
+\alias{create_term_match_table}
+\title{create term matching Table}
+\usage{
+create_term_match_table(instrument_list = c("Thermo_EASY-nLC",
+  "Q Exactive_Plus_-_Orbitrap_MS"), origin_key = "")
+}
+\arguments{
+\item{instrument_list}{list of instruments in the raw file, get it with "instrument_names()".}
+
+\item{origin_key}{Specifies which information is required.
+If empty, all information is used.
+"jpr_guidelines_ms" for the requirements of the Journal of Proteome Research.
+"miape" for The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.}
+}
+\value{
+A table needed to extract the meta data with match_terms().
+}
+\description{
+create term matching Table
+}
+\examples{
+term_matching_table <- create_term_match_table(
+  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
+  origin_key = "jpr_guidelines_ms")
+
+}
diff --git a/man/files_in_group.Rd b/man/files_in_group.Rd
index a1b7bbb..bbeec8e 100644
--- a/man/files_in_group.Rd
+++ b/man/files_in_group.Rd
@@ -1,27 +1,27 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/additional_functions.R
-\name{files_in_group}
-\alias{files_in_group}
-\title{Filenames of one group}
-\usage{
-files_in_group(json, group_number)
-}
-\arguments{
-\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
-
-\item{group_number}{An index that determines the group.}
-}
-\value{
-A list of filenames belonging to the choosen group.
-}
-\description{
-Filenames of one group
-}
-\examples{
-
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-files_in_group(json, 1)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/additional_functions.R
+\name{files_in_group}
+\alias{files_in_group}
+\title{Filenames of one group}
+\usage{
+files_in_group(json, group_number)
+}
+\arguments{
+\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
+
+\item{group_number}{An index that determines the group.}
+}
+\value{
+A list of filenames belonging to the choosen group.
+}
+\description{
+Filenames of one group
+}
+\examples{
+
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+files_in_group(json, 1)
+
+}
diff --git a/man/flatten_json.Rd b/man/flatten_json.Rd
index c636432..0236fd3 100644
--- a/man/flatten_json.Rd
+++ b/man/flatten_json.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/load_meta_functions.R
-\name{flatten_json}
-\alias{flatten_json}
-\title{flattening JSON}
-\usage{
-flatten_json(json)
-}
-\arguments{
-\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
-}
-\value{
-A flattened Json for better access.
-}
-\description{
-flattening JSON
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load_meta_functions.R
+\name{flatten_json}
+\alias{flatten_json}
+\title{flattening JSON}
+\usage{
+flatten_json(json)
+}
+\arguments{
+\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
+}
+\value{
+A flattened Json for better access.
+}
+\description{
+flattening JSON
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+}
diff --git a/man/gradient_as_string.Rd b/man/gradient_as_string.Rd
index 96ffdaf..5f8e6f2 100644
--- a/man/gradient_as_string.Rd
+++ b/man/gradient_as_string.Rd
@@ -1,19 +1,19 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gradient_functions.R
-\name{gradient_as_string}
-\alias{gradient_as_string}
-\title{Gradient table to string.}
-\usage{
-gradient_as_string(flat_json, group_number)
-}
-\arguments{
-\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
-
-\item{group_number}{An index that determines the group.}
-}
-\value{
-Gradient information as sentence.
-}
-\description{
-Gradient table to string.
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gradient_functions.R
+\name{gradient_as_string}
+\alias{gradient_as_string}
+\title{Gradient table to string.}
+\usage{
+gradient_as_string(flat_json, group_number)
+}
+\arguments{
+\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
+
+\item{group_number}{An index that determines the group.}
+}
+\value{
+Gradient information as sentence.
+}
+\description{
+Gradient table to string.
+}
diff --git a/man/gradient_tables.Rd b/man/gradient_tables.Rd
index 2a2ddf6..1ffbbdc 100644
--- a/man/gradient_tables.Rd
+++ b/man/gradient_tables.Rd
@@ -1,28 +1,28 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gradient_functions.R
-\name{gradient_tables}
-\alias{gradient_tables}
-\title{Create a list with all gradient tables.}
-\usage{
-gradient_tables(flat_json, lc_pump = "Thermo EASY-nLC")
-}
-\arguments{
-\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
-
-\item{lc_pump}{Name of the used lc pump, default = "Thermo EASY-nLC"}
-}
-\value{
-List of gradients for all groups
-}
-\description{
-Create a list with all gradient tables.
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-gradient_tables(flat_json)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gradient_functions.R
+\name{gradient_tables}
+\alias{gradient_tables}
+\title{Create a list with all gradient tables.}
+\usage{
+gradient_tables(flat_json, lc_pump = "Thermo EASY-nLC")
+}
+\arguments{
+\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
+
+\item{lc_pump}{Name of the used lc pump, default = "Thermo EASY-nLC"}
+}
+\value{
+List of gradients for all groups
+}
+\description{
+Create a list with all gradient tables.
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+gradient_tables(flat_json)
+
+}
diff --git a/man/group_count.Rd b/man/group_count.Rd
index f32b4fa..09e144b 100644
--- a/man/group_count.Rd
+++ b/man/group_count.Rd
@@ -1,24 +1,24 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/additional_functions.R
-\name{group_count}
-\alias{group_count}
-\title{Number of groups in the json file}
-\usage{
-group_count(json)
-}
-\arguments{
-\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
-}
-\value{
-Count of groups in the JSON file.
-}
-\description{
-Number of groups in the json file
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-group_count(json)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/additional_functions.R
+\name{group_count}
+\alias{group_count}
+\title{Number of groups in the json file}
+\usage{
+group_count(json)
+}
+\arguments{
+\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
+}
+\value{
+Count of groups in the JSON file.
+}
+\description{
+Number of groups in the json file
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+group_count(json)
+
+}
diff --git a/man/instrument_names.Rd b/man/instrument_names.Rd
index 30d9778..23dc0f9 100644
--- a/man/instrument_names.Rd
+++ b/man/instrument_names.Rd
@@ -1,26 +1,26 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/additional_functions.R
-\name{instrument_names}
-\alias{instrument_names}
-\title{Get instrument names}
-\usage{
-instrument_names(json, group_number)
-}
-\arguments{
-\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
-
-\item{group_number}{An index that determines the group.}
-}
-\value{
-A list of instruments used in the choosen group.
-}
-\description{
-Get instrument names
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-instrument_names(json, 1)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/additional_functions.R
+\name{instrument_names}
+\alias{instrument_names}
+\title{Get instrument names}
+\usage{
+instrument_names(json, group_number)
+}
+\arguments{
+\item{json}{A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.}
+
+\item{group_number}{An index that determines the group.}
+}
+\value{
+A list of instruments used in the choosen group.
+}
+\description{
+Get instrument names
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+instrument_names(json, 1)
+
+}
diff --git a/man/match_terms.Rd b/man/match_terms.Rd
index 6674808..cefb314 100644
--- a/man/match_terms.Rd
+++ b/man/match_terms.Rd
@@ -1,32 +1,32 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/term_matching_functions.R
-\name{match_terms}
-\alias{match_terms}
-\title{Match terms for all groups}
-\usage{
-match_terms(flat_json, term_matching_table)
-}
-\arguments{
-\item{flat_json}{A flattened JSON file, created by "flatten_json()".}
-
-\item{term_matching_table}{A table containing handles, created by "read_tm_table()".}
-}
-\value{
-A vector containing tables with meta data for each group of raw files.
-}
-\description{
-Match terms for all groups
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-term_matching_table <- create_term_match_table(
-  instrument_list = instrument_names(json, 1),
-  origin_key = "jpr_guidelines_ms")
-
-vector_of_group_tables <- match_terms(flat_json, term_matching_table)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/term_matching_functions.R
+\name{match_terms}
+\alias{match_terms}
+\title{Match terms for all groups}
+\usage{
+match_terms(flat_json, term_matching_table)
+}
+\arguments{
+\item{flat_json}{A flattened JSON file, created by "flatten_json()".}
+
+\item{term_matching_table}{A table containing handles, created by "read_tm_table()".}
+}
+\value{
+A vector containing tables with meta data for each group of raw files.
+}
+\description{
+Match terms for all groups
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+term_matching_table <- create_term_match_table(
+  instrument_list = instrument_names(json, 1),
+  origin_key = "jpr_guidelines_ms")
+
+vector_of_group_tables <- match_terms(flat_json, term_matching_table)
+
+}
diff --git a/man/one_gradient_table.Rd b/man/one_gradient_table.Rd
index 5ad1c41..78a1cfa 100644
--- a/man/one_gradient_table.Rd
+++ b/man/one_gradient_table.Rd
@@ -1,30 +1,30 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gradient_functions.R
-\name{one_gradient_table}
-\alias{one_gradient_table}
-\title{Gradient.}
-\usage{
-one_gradient_table(flat_json, group_number, lc_pump = "Thermo EASY-nLC")
-}
-\arguments{
-\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
-
-\item{group_number}{An index that determines the group.}
-
-\item{lc_pump}{Name of the used lc_pump, default = "Thermo EASY-nLC".}
-}
-\value{
-A table with gradient.
-}
-\description{
-Gradient.
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-one_gradient_table(flat_json, 1)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gradient_functions.R
+\name{one_gradient_table}
+\alias{one_gradient_table}
+\title{Gradient.}
+\usage{
+one_gradient_table(flat_json, group_number, lc_pump = "Thermo EASY-nLC")
+}
+\arguments{
+\item{flat_json}{A flattened JSON file, created by "prepare_json()".}
+
+\item{group_number}{An index that determines the group.}
+
+\item{lc_pump}{Name of the used lc_pump, default = "Thermo EASY-nLC".}
+}
+\value{
+A table with gradient.
+}
+\description{
+Gradient.
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+one_gradient_table(flat_json, 1)
+
+}
diff --git a/man/one_group_match_terms.Rd b/man/one_group_match_terms.Rd
index f21c626..fbe7f33 100644
--- a/man/one_group_match_terms.Rd
+++ b/man/one_group_match_terms.Rd
@@ -1,34 +1,34 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/term_matching_functions.R
-\name{one_group_match_terms}
-\alias{one_group_match_terms}
-\title{Match terms for one group}
-\usage{
-one_group_match_terms(flat_json, term_matching_table, group_number)
-}
-\arguments{
-\item{flat_json}{A flattened JSON file, created by "flatten_json()".}
-
-\item{term_matching_table}{A table containing handles, created by "read_tm_table()".}
-
-\item{group_number}{An index that determines the group.}
-}
-\value{
-Table with meta data for the choosen group of raw files.
-}
-\description{
-Match terms for one group
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-term_matching_table <- create_term_match_table(
-  instrument_list = instrument_names(json, 1),
-  origin_key = "jpr_guidelines_ms")
-
-meta_data_table <- one_group_match_terms(flat_json, term_matching_table, 1)
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/term_matching_functions.R
+\name{one_group_match_terms}
+\alias{one_group_match_terms}
+\title{Match terms for one group}
+\usage{
+one_group_match_terms(flat_json, term_matching_table, group_number)
+}
+\arguments{
+\item{flat_json}{A flattened JSON file, created by "flatten_json()".}
+
+\item{term_matching_table}{A table containing handles, created by "read_tm_table()".}
+
+\item{group_number}{An index that determines the group.}
+}
+\value{
+Table with meta data for the choosen group of raw files.
+}
+\description{
+Match terms for one group
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+term_matching_table <- create_term_match_table(
+  instrument_list = instrument_names(json, 1),
+  origin_key = "jpr_guidelines_ms")
+
+meta_data_table <- one_group_match_terms(flat_json, term_matching_table, 1)
+
+}
diff --git a/man/save_all_groups.Rd b/man/save_all_groups.Rd
index b7f0814..de69c22 100644
--- a/man/save_all_groups.Rd
+++ b/man/save_all_groups.Rd
@@ -1,33 +1,33 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output_functions.R
-\name{save_all_groups}
-\alias{save_all_groups}
-\title{write all groups to files}
-\usage{
-save_all_groups(groups_vector, output_path)
-}
-\arguments{
-\item{groups_vector}{A List with a table for each group.}
-
-\item{output_path}{A path and filename where to write the outputfiles. [output_path]_group_[index].txt}
-}
-\description{
-write all groups to files
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-term_matching_table <- create_term_match_table(
-  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
-  origin_key = "jpr_guidelines_ms")
-
-vector_of_group_tables <- match_terms(flat_json, term_matching_table)
-
-(partial_path_for_output <- tempfile())
-save_all_groups(vector_of_group_tables, partial_path_for_output)
-head(readLines(paste0(partial_path_for_output, '_group_1.txt')))
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output_functions.R
+\name{save_all_groups}
+\alias{save_all_groups}
+\title{write all groups to files}
+\usage{
+save_all_groups(groups_vector, output_path)
+}
+\arguments{
+\item{groups_vector}{A List with a table for each group.}
+
+\item{output_path}{A path and filename where to write the outputfiles. [output_path]_group_[index].txt}
+}
+\description{
+write all groups to files
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+term_matching_table <- create_term_match_table(
+  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
+  origin_key = "jpr_guidelines_ms")
+
+vector_of_group_tables <- match_terms(flat_json, term_matching_table)
+
+(partial_path_for_output <- tempfile())
+save_all_groups(vector_of_group_tables, partial_path_for_output)
+head(readLines(paste0(partial_path_for_output, '_group_1.txt')))
+
+}
diff --git a/man/save_group_table.Rd b/man/save_group_table.Rd
index 166c2af..0a1bcf1 100644
--- a/man/save_group_table.Rd
+++ b/man/save_group_table.Rd
@@ -1,35 +1,35 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/output_functions.R
-\name{save_group_table}
-\alias{save_group_table}
-\title{write table of specified group to file}
-\usage{
-save_group_table(groups_vector, output_path, group_number)
-}
-\arguments{
-\item{groups_vector}{A List with a table for each group.}
-
-\item{output_path}{A path and filename where to write the output.}
-
-\item{group_number}{An index that determines the group.}
-}
-\description{
-write table of specified group to file
-}
-\examples{
-# Real-time JSON-generation: `json <- generate_json(data)`
-json <- MARMoSET::testfile_json
-
-flat_json <- flatten_json(json)
-
-term_matching_table <- create_term_match_table(
-  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
-  origin_key = "jpr_guidelines_ms")
-
-vector_of_group_tables <- match_terms(flat_json, term_matching_table)
-
-(partial_path_for_output <- tempfile())
-save_group_table(vector_of_group_tables, partial_path_for_output, 1)
-head(readLines(paste(partial_path_for_output, 'txt', sep = '.')))
-
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/output_functions.R
+\name{save_group_table}
+\alias{save_group_table}
+\title{write table of specified group to file}
+\usage{
+save_group_table(groups_vector, output_path, group_number)
+}
+\arguments{
+\item{groups_vector}{A List with a table for each group.}
+
+\item{output_path}{A path and filename where to write the output.}
+
+\item{group_number}{An index that determines the group.}
+}
+\description{
+write table of specified group to file
+}
+\examples{
+# Real-time JSON-generation: `json <- generate_json(data)`
+json <- MARMoSET::testfile_json
+
+flat_json <- flatten_json(json)
+
+term_matching_table <- create_term_match_table(
+  instrument_list = c("Thermo_EASY-nLC", "Q_Exactive_-_Orbitrap_MS"),
+  origin_key = "jpr_guidelines_ms")
+
+vector_of_group_tables <- match_terms(flat_json, term_matching_table)
+
+(partial_path_for_output <- tempfile())
+save_group_table(vector_of_group_tables, partial_path_for_output, 1)
+head(readLines(paste(partial_path_for_output, 'txt', sep = '.')))
+
+}
diff --git a/man/tmt_list.Rd b/man/tmt_list.Rd
index 4da4bfe..167c7de 100644
--- a/man/tmt_list.Rd
+++ b/man/tmt_list.Rd
@@ -1,21 +1,21 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{tmt_list}
-\alias{tmt_list}
-\title{Term matching tables for different instruments}
-\format{A list of data frames:
-\describe{
-  \item{Q_Exactive_Plus_-_Orbitrap_MS}{MS instrument}
-  \item{Q_Exactive_HF_-_Orbitrap_MS}{MS instrument}
-  \item{Q_Exactive_-_Orbitrap_MS}{MS instrument}
-  \item{Thermo_EASY-nLC}{LC pump}
-  ...
-}}
-\usage{
-tmt_list
-}
-\description{
-Term matching tables for different instruments
-}
-\keyword{datasets}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{tmt_list}
+\alias{tmt_list}
+\title{Term matching tables for different instruments}
+\format{A list of data frames:
+\describe{
+  \item{Q_Exactive_Plus_-_Orbitrap_MS}{MS instrument}
+  \item{Q_Exactive_HF_-_Orbitrap_MS}{MS instrument}
+  \item{Q_Exactive_-_Orbitrap_MS}{MS instrument}
+  \item{Thermo_EASY-nLC}{LC pump}
+  ...
+}}
+\usage{
+tmt_list
+}
+\description{
+Term matching tables for different instruments
+}
+\keyword{datasets}
diff --git a/man/tmt_one_instrument.Rd b/man/tmt_one_instrument.Rd
index 3d20b50..f28f22c 100644
--- a/man/tmt_one_instrument.Rd
+++ b/man/tmt_one_instrument.Rd
@@ -1,22 +1,22 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/load_term_matching_table_function.R
-\name{tmt_one_instrument}
-\alias{tmt_one_instrument}
-\title{read tmt table for one instrument}
-\usage{
-tmt_one_instrument(instrument, origin_key = "all")
-}
-\arguments{
-\item{instrument}{Name of the instrument in tmt_list.}
-
-\item{origin_key}{Specifies which information is required.
-If empty, all information is used.
-"jpr_guidelines_ms" for the requirements of the Journal of Proteome Research.
-"miape" for The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.}
-}
-\value{
-Table with tmt part for this instrument.
-}
-\description{
-read tmt table for one instrument
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/load_term_matching_table_function.R
+\name{tmt_one_instrument}
+\alias{tmt_one_instrument}
+\title{read tmt table for one instrument}
+\usage{
+tmt_one_instrument(instrument, origin_key = "all")
+}
+\arguments{
+\item{instrument}{Name of the instrument in tmt_list.}
+
+\item{origin_key}{Specifies which information is required.
+If empty, all information is used.
+"jpr_guidelines_ms" for the requirements of the Journal of Proteome Research.
+"miape" for The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative.}
+}
+\value{
+Table with tmt part for this instrument.
+}
+\description{
+read tmt table for one instrument
+}