diff --git a/R/clean_DIANN.R b/R/clean_DIANN.R index 43de34475..130066a98 100644 --- a/R/clean_DIANN.R +++ b/R/clean_DIANN.R @@ -4,42 +4,49 @@ #' @return data.table #' @importFrom stats na.omit #' @keywords internal -.cleanRawDIANN <- function(msstats_object, MBR = TRUE, +.cleanRawDIANN <- function(msstats_object, MBR = TRUE, quantificationColumn = "FragmentQuantCorrected", global_qvalue_cutoff = 0.01, - qvalue_cutoff = 0.01, + qvalue_cutoff = 0.01, pg_qvalue_cutoff = 0.01, - calculateAnomalyScores = FALSE, - anomalyModelFeatures = c()) { + calculateAnomalyScores = FALSE, + anomalyModelFeatures = c(), + labeledAminoAcids = NULL) { dn_input <- getInputFile(msstats_object, "input") dn_input <- data.table::as.data.table(dn_input) - + # Process quantification columns quantificationColumn <- .cleanDIANNProcessQuantificationColumns(dn_input, quantificationColumn) - + # Add missing columns dn_input <- .cleanDIANNAddMissingColumns(dn_input) - + + has_channel <- !is.null(labeledAminoAcids) && "Channel" %in% colnames(dn_input) + # Select required columns dn_input <- .cleanDIANNSelectRequiredColumns(dn_input, quantificationColumn, MBR, calculateAnomalyScores, - anomalyModelFeatures) - + anomalyModelFeatures, + has_channel = has_channel) + # Split concatenated values dn_input <- .cleanDIANNSplitConcatenatedValues(dn_input, quantificationColumn) - + # Process fragment information dn_input <- .cleanDIANNProcessFragmentInfo(dn_input, quantificationColumn) - + # Clean and filter data - dn_input <- .cleanDIANNCleanAndFilterData(dn_input, MBR, quantificationColumn, + dn_input <- .cleanDIANNCleanAndFilterData(dn_input, MBR, quantificationColumn, global_qvalue_cutoff, - qvalue_cutoff, + qvalue_cutoff, pg_qvalue_cutoff) - + # Rename columns dn_input <- .cleanDIANNRenameColumns(dn_input, quantificationColumn) - + + # Assign IsotopeLabelType for protein turnover + dn_input <- .assignDIANNIsotopeLabelType(dn_input, labeledAminoAcids, has_channel) + .logSuccess("DIANN", "clean") dn_input } @@ -84,17 +91,22 @@ #' @noRd .cleanDIANNSelectRequiredColumns <- function(dn_input, quantificationColumn, MBR, calculateAnomalyScores, - anomalyModelFeatures) { - base_cols <- c('ProteinNames', 'StrippedSequence', 'ModifiedSequence', - 'PrecursorCharge', quantificationColumn, 'QValue', + anomalyModelFeatures, + has_channel = FALSE) { + base_cols <- c('ProteinNames', 'StrippedSequence', 'ModifiedSequence', + 'PrecursorCharge', quantificationColumn, 'QValue', 'PrecursorMz', 'FragmentInfo', 'Run') - + + if (has_channel) { + base_cols <- c(base_cols, 'Channel') + } + mbr_cols <- if (MBR) { c('LibQValue', 'LibPGQValue') } else { c('GlobalQValue', 'GlobalPGQValue') } - + qual_cols <- if (calculateAnomalyScores) { anomalyModelFeatures } else { @@ -207,6 +219,70 @@ return(dn_input) } +#' Assign IsotopeLabelType for DIANN protein turnover workflows. +#' +#' Dispatches to one of two classification paths depending on \code{has_channel}: +#' +#' \strong{Channel-based path} (\code{has_channel = TRUE}): \code{Channel} +#' values are mapped directly to \code{IsotopeLabelType} (\code{"H"} → +#' \code{"H"}, \code{"L"} → \code{"L"}, anything else → \code{NA}), and the +#' \code{Channel} column is then dropped. \code{labeledAminoAcids} acts solely +#' as the opt-in flag that enables this path; the amino acid codes are +#' \strong{not} used to validate or filter \code{ModifiedSequence}. +#' +#' \strong{ModifiedSequence-parsing path} (\code{has_channel = FALSE}): +#' \code{PeptideSequence} (the retained \code{ModifiedSequence}) is matched +#' against SILAC suffixes of the form \code{(SILAC--H)} or +#' \code{(SILAC--L)}, where \code{} is any code in +#' \code{labeledAminoAcids}. Sequences carrying neither suffix receive +#' \code{IsotopeLabelType = NA}. The SILAC suffix is stripped from +#' \code{PeptideSequence} after classification. +#' +#' @param dn_input \code{data.table} after column renaming. +#' @param labeledAminoAcids Character vector of single-letter amino acid codes +#' (e.g. \code{c("K")} or \code{c("K", "R")}), or \code{NULL} to skip +#' protein-turnover mode entirely (backwards-compatible default). +#' @param has_channel Logical; \code{TRUE} when the raw input contained a +#' \code{Channel} column that was retained through +#' \code{.cleanDIANNSelectRequiredColumns}. +#' @return \code{dn_input} with \code{IsotopeLabelType} column added (and +#' \code{Channel} removed when \code{has_channel} is \code{TRUE}). +#' @keywords internal +#' @noRd +.assignDIANNIsotopeLabelType <- function(dn_input, labeledAminoAcids, has_channel) { + IsotopeLabelType = Channel = PeptideSequence = NULL + + if (is.null(labeledAminoAcids)) { + return(dn_input) + } + + if (has_channel) { + dn_input[, IsotopeLabelType := data.table::fcase( + Channel == "H", "H", + Channel == "L", "L", + default = NA_character_ + )] + dn_input[, Channel := NULL] + } else { + aa_pattern <- paste0(labeledAminoAcids, collapse = "|") + heavy_regex <- paste0("\\(SILAC-(?:", aa_pattern, ")-H\\)") + light_regex <- paste0("\\(SILAC-(?:", aa_pattern, ")-L\\)") + strip_regex <- paste0("\\(SILAC-(?:", aa_pattern, ")-[HL]\\)") + + dn_input <- .classifyIsotopeLabelType(dn_input, heavy_regex, light_regex) + dn_input[, PeptideSequence := gsub(strip_regex, "", PeptideSequence, perl = TRUE)] + } + + if (all(is.na(dn_input[["IsotopeLabelType"]]))) { + warning("labeledAminoAcids was provided but no rows were classified as H or L. ", + "Check that the input contains either a Channel column with H/L values ", + "or ModifiedSequence entries with (SILAC--H)/(SILAC--L) suffixes.") + } + + dn_input +} + + #' Rename columns to standardized names #' @param dn_input data.table input #' @param quantificationColumn quantification column name diff --git a/R/clean_Spectronaut.R b/R/clean_Spectronaut.R index 4729683ff..ebf7cc98e 100644 --- a/R/clean_Spectronaut.R +++ b/R/clean_Spectronaut.R @@ -183,32 +183,25 @@ #' @keywords internal #' @noRd .assignSpectronautIsotopeLabelType = function(spec_input, heavyLabels) { - IsotopeLabelType = PeptideSequence = StrippedSequence = NULL + PeptideSequence = NULL if (is.null(heavyLabels)) { return(spec_input) } - + bare_amino_acids = sub("\\[.*\\]", "", heavyLabels) - bare_amino_acids_pattern = paste0(bare_amino_acids, collapse = "|") - heavy_pattern = paste0(heavyLabels, collapse = "|") - heavy_brackets_escaped_pattern = paste( - gsub("([\\[\\]])", "\\\\\\1", heavy_pattern, perl = TRUE), + labeled_aa_regex = paste0(bare_amino_acids, collapse = "|") + heavy_regex = paste( + gsub("([\\[\\]])", "\\\\\\1", heavyLabels, perl = TRUE), collapse = "|" ) - - spec_input[, StrippedSequence := gsub("\\[.*?\\]", "", PeptideSequence)] - - spec_input[, IsotopeLabelType := data.table::fcase( - grepl(heavy_brackets_escaped_pattern, PeptideSequence, perl = TRUE), "H", - grepl(bare_amino_acids_pattern, StrippedSequence, perl = TRUE), "L", - default = NA_character_ - )] - - spec_input[, StrippedSequence := NULL] - + + spec_input = .classifyIsotopeLabelType(spec_input, heavy_regex, + labeled_aa_regex = labeled_aa_regex) + for (i in seq_along(heavyLabels)) { escaped = gsub("([\\[\\]])", "\\\\\\1", heavyLabels[i], perl = TRUE) - spec_input[, PeptideSequence := gsub(escaped, bare_amino_acids[i], PeptideSequence, perl = TRUE)] + spec_input[, PeptideSequence := gsub(escaped, bare_amino_acids[i], + PeptideSequence, perl = TRUE)] } spec_input } diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R index 833990f68..78f3f1630 100644 --- a/R/converters_DIANNtoMSstatsFormat.R +++ b/R/converters_DIANNtoMSstatsFormat.R @@ -19,8 +19,33 @@ #' @param removeFewMeasurements should proteins with few measurements be removed #' @param removeOxidationMpeptides should peptides with oxidation be removed #' @param removeProtein_with1Feature should proteins with a single feature be removed +#' @param labeledAminoAcids Character vector of single-letter amino acid codes +#' that carry the SILAC label in protein turnover experiments, e.g. +#' \code{c("K")} or \code{c("K", "R")}. Supplying this vector opts in to +#' protein-turnover mode; the exact amino acids determine behaviour only in the +#' \code{ModifiedSequence}-parsing path described below. +#' +#' \strong{Channel-based path} (DIA-NN 2.x exports that include a +#' \code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +#' \emph{and} the input contains a \code{Channel} column, \code{Channel} values +#' are mapped directly to \code{IsotopeLabelType} (\code{"H"} → \code{"H"}, +#' \code{"L"} → \code{"L"}, anything else → \code{NA}). The amino acid codes +#' in \code{labeledAminoAcids} are \strong{not} used to validate or filter +#' \code{ModifiedSequence} in this path. +#' +#' \strong{ModifiedSequence-parsing path} (DIA-NN 1.x exports without a +#' \code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +#' and no \code{Channel} column is present, each \code{ModifiedSequence} is +#' inspected for SILAC suffixes of the form \code{(SILAC--H)} or +#' \code{(SILAC--L)}, where \code{} is one of the supplied amino acid +#' codes. Matching sequences are classified as \code{"H"} or \code{"L"}; +#' sequences carrying neither suffix receive \code{IsotopeLabelType = NA}. +#' The SILAC suffix is then stripped from \code{PeptideSequence}. +#' +#' When \code{NULL} (default), protein-turnover mode is disabled and all +#' peptides receive \code{IsotopeLabelType = "Light"}. #' @param quantificationColumn Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x. -#' Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. +#' Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. #' Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity. #' @param calculateAnomalyScores Default is FALSE. If TRUE, will run anomaly detection model and calculate anomaly scores for each feature. Used downstream to weigh measurements in differential analysis. #' @param anomalyModelFeatures character vector of quality metric column names to be used as features in the anomaly detection model. List must not be empty if calculateAnomalyScores=TRUE. @@ -63,19 +88,20 @@ DIANNtoMSstatsFormat = function( input, annotation = NULL, global_qvalue_cutoff = 0.01, - qvalue_cutoff = 0.01, + qvalue_cutoff = 0.01, pg_qvalue_cutoff = 0.01, - useUniquePeptide = TRUE, + useUniquePeptide = TRUE, removeFewMeasurements = TRUE, - removeOxidationMpeptides = TRUE, + removeOxidationMpeptides = TRUE, removeProtein_with1Feature = TRUE, - MBR = TRUE, + MBR = TRUE, + labeledAminoAcids = NULL, quantificationColumn = "FragmentQuantCorrected", calculateAnomalyScores=FALSE, anomalyModelFeatures=c(), anomalyModelFeatureTemporal=c(), removeMissingFeatures=.5, anomalyModelFeatureCount=100, - runOrder=NULL, n_trees=100, max_depth="auto", numberOfCores=1, - use_log_file = TRUE, append = FALSE, + runOrder=NULL, n_trees=100, max_depth="auto", numberOfCores=1, + use_log_file = TRUE, append = FALSE, verbose = TRUE, log_file_path = NULL, ...) { MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, @@ -86,42 +112,46 @@ DIANNtoMSstatsFormat = function( input = MSstatsConvert::MSstatsImport(list(input = input), "MSstats", "DIANN") - input = MSstatsConvert::MSstatsClean(input, MBR = MBR, + input = MSstatsConvert::MSstatsClean(input, MBR = MBR, quantificationColumn = quantificationColumn, global_qvalue_cutoff = global_qvalue_cutoff, - qvalue_cutoff = qvalue_cutoff, + qvalue_cutoff = qvalue_cutoff, pg_qvalue_cutoff = pg_qvalue_cutoff, - calculateAnomalyScores = calculateAnomalyScores, - anomalyModelFeatures = anomalyModelFeatures) + calculateAnomalyScores = calculateAnomalyScores, + anomalyModelFeatures = anomalyModelFeatures, + labeledAminoAcids = labeledAminoAcids) annotation = MSstatsConvert::MSstatsMakeAnnotation(input, annotation) - + decoy_filter = list(col_name = "ProteinName", pattern = c("DECOY", "Decoys"), - filter = T, + filter = T, drop_column = FALSE) oxidation_filter = list(col_name = "PeptideSequence", pattern = "\\(UniMod\\:35\\)", filter = removeOxidationMpeptides, drop_column = FALSE) - + feature_columns = c("PeptideSequence", "PrecursorCharge", "FragmentIon", "ProductCharge") - # browser() + preprocess_feature_columns = if ("IsotopeLabelType" %in% colnames(input)) + c(feature_columns, "IsotopeLabelType") else feature_columns + fill_isotope_label_type = if ("IsotopeLabelType" %in% colnames(input)) + list() else list("IsotopeLabelType" = "Light") + input = MSstatsConvert::MSstatsPreprocess( - input, - annotation, - feature_columns, + input, + annotation, + preprocess_feature_columns, remove_shared_peptides = useUniquePeptide, remove_single_feature_proteins = removeProtein_with1Feature, exact_filtering = NULL, - pattern_filtering = list(decoy = decoy_filter, + pattern_filtering = list(decoy = decoy_filter, oxidation = oxidation_filter), aggregate_isotopic = FALSE, feature_cleaning = list( remove_features_with_few_measurements = removeFewMeasurements, summarize_multiple_psms = max), - columns_to_fill = list(Fraction = 1, - IsotopeLabelType = "Light"), + columns_to_fill = c(list(Fraction = 1), fill_isotope_label_type), anomaly_metrics = anomalyModelFeatures) input[, Intensity := ifelse(Intensity == 0, NA, Intensity)] # browser() diff --git a/R/utils_clean_features.R b/R/utils_clean_features.R index 8ba1045f0..c1c7094aa 100644 --- a/R/utils_clean_features.R +++ b/R/utils_clean_features.R @@ -309,6 +309,60 @@ } +#' Classify IsotopeLabelType from peptide sequence patterns. +#' +#' Shared core logic for protein turnover workflows in both Spectronaut and +#' DIANN converters. Each peptide is classified as heavy (\code{"H"}), light +#' (\code{"L"}), or unlabeled (\code{NA}) by matching regex patterns against +#' the \code{PeptideSequence} column. +#' +#' Two modes are supported: +#' \describe{ +#' \item{Spectronaut mode}{Pass \code{labeled_aa_regex}. The sequence is +#' first stripped of all bracket modifications; light is inferred when the +#' bare labeled amino acid is present but the heavy bracket form is absent.} +#' \item{DIANN mode}{Pass \code{light_regex}. Both heavy and light patterns +#' are matched directly against the modified sequence; absence of either +#' yields \code{NA}.} +#' } +#' +#' @param dt \code{data.table} with a \code{PeptideSequence} column. +#' @param heavy_regex Perl-compatible regex matching heavy-labeled sequences. +#' @param light_regex Perl-compatible regex explicitly matching light-labeled +#' sequences. Required for DIANN mode; must be non-\code{NULL}. +#' @param labeled_aa_regex Perl-compatible regex for bare labeled amino acids +#' applied to the bracket-stripped sequence to detect light peptides. +#' Required for Spectronaut mode; must be non-\code{NULL}. +#' Exactly one of \code{light_regex} and \code{labeled_aa_regex} must be +#' supplied. +#' @return \code{dt} with \code{IsotopeLabelType} column added or updated. +#' @keywords internal +#' @noRd +.classifyIsotopeLabelType = function(dt, heavy_regex, + light_regex = NULL, + labeled_aa_regex = NULL) { + IsotopeLabelType = PeptideSequence = StrippedSequence = NULL + + if (!is.null(labeled_aa_regex)) { + dt[, StrippedSequence := gsub("\\[.*?\\]", "", PeptideSequence)] + dt[, IsotopeLabelType := data.table::fcase( + grepl(heavy_regex, PeptideSequence, perl = TRUE), "H", + grepl(labeled_aa_regex, StrippedSequence, perl = TRUE), "L", + default = NA_character_ + )] + dt[, StrippedSequence := NULL] + } else if (!is.null(light_regex)) { + dt[, IsotopeLabelType := data.table::fcase( + grepl(heavy_regex, PeptideSequence, perl = TRUE), "H", + grepl(light_regex, PeptideSequence, perl = TRUE), "L", + default = NA_character_ + )] + } + + dt +} + + #' Fix invalid intensities: infinite to NA, between 0 and 1 to 0 #' @param input data.table #' @return data.table diff --git a/inst/tinytest/raw_data/DIANN/PXD055942.parquet b/inst/tinytest/raw_data/DIANN/PXD055942.parquet new file mode 100644 index 000000000..c576365a5 Binary files /dev/null and b/inst/tinytest/raw_data/DIANN/PXD055942.parquet differ diff --git a/inst/tinytest/raw_data/DIANN/annotation_PXD055942.csv b/inst/tinytest/raw_data/DIANN/annotation_PXD055942.csv new file mode 100644 index 000000000..b83975703 --- /dev/null +++ b/inst/tinytest/raw_data/DIANN/annotation_PXD055942.csv @@ -0,0 +1,25 @@ +"Run","Condition","BioReplicate" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_0d_1","0 day","Replicate 1 0 day" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_0d_1","0 day","Replicate 1 0 day" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_0d_1","0 day","Replicate 1 0 day" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_0d_1","0 day","Replicate 1 0 day" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_0d_2","0 day","Replicate 2 0 day" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_0d_2","0 day","Replicate 2 0 day" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_0d_2","0 day","Replicate 2 0 day" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_0d_2","0 day","Replicate 2 0 day" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_8d_1","8 days","Replicate 1 8 days" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_8d_1","8 days","Replicate 1 8 days" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_8d_1","8 days","Replicate 1 8 days" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_8d_1","8 days","Replicate 1 8 days" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_32d_1","32 days","Replicate 1 32 days" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_32d_1","32 days","Replicate 1 32 days" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_32d_1","32 days","Replicate 1 32 days" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_32d_1","32 days","Replicate 1 32 days" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_8d_2","8 days","Replicate 2 8 days" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_8d_2","8 days","Replicate 2 8 days" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_8d_2","8 days","Replicate 2 8 days" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_8d_2","8 days","Replicate 2 8 days" +"20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_32d_2","32 days","Replicate 2 32 days" +"20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_32d_2","32 days","Replicate 2 32 days" +"20210805_BoxCarmax3rd_wideMS1_JM_pSIL_pro_heart_32d_2","32 days","Replicate 2 32 days" +"20210805_BoxCarmax4th_wideMS1_JM_pSIL_pro_heart_32d_2","32 days","Replicate 2 32 days" diff --git a/inst/tinytest/raw_data/DIANN/annotation_silac.csv b/inst/tinytest/raw_data/DIANN/annotation_silac.csv new file mode 100644 index 000000000..dd2156992 --- /dev/null +++ b/inst/tinytest/raw_data/DIANN/annotation_silac.csv @@ -0,0 +1,11 @@ +"Run","Condition","BioReplicate" +"dAL_AT_Long_B1",10,1 +"dAL_AT_Long_B10",10,2 +"dAL_AT_Long_B2",10,3 +"dAL_AT_Long_B3",5,4 +"dAL_AT_Long_B4",5,5 +"dAL_AT_Long_B5",5,6 +"dAL_AT_Long_B6",5,7 +"dAL_AT_Long_B7",5,8 +"dAL_AT_Long_B8",5,9 +"dAL_AT_Long_B9",10,10 diff --git a/inst/tinytest/raw_data/DIANN/diann_input_silac.csv b/inst/tinytest/raw_data/DIANN/diann_input_silac.csv new file mode 100644 index 000000000..f3a0b1643 --- /dev/null +++ b/inst/tinytest/raw_data/DIANN/diann_input_silac.csv @@ -0,0 +1,51 @@ 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+"G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\aleduc\miceotopes\Bulk\dAL_AT_Long_B8.raw","dAL_AT_Long_B8","Q6NZL0","Q6NZL0","SOGA3_MOUSE","Soga3",10869921,20067288,6876724.5,10869921,20067288,6876724.5,6176264.5,"AAAAAAAAQMHTK(SILAC-K-L)","AAAAAAAAQMHTK","AAAAAAAAQMHTK(SILAC-K-L)2",2,2.799317008e-05,0.0001256719988,0.01398449857,0.0001751006785,0.000171703301,0.0001358142035,0.0001723840687,0,1,39374.10938,77272.54688,33421.18359,0.3308399916,139349.5312,0.9095945954,16.17643166,15.93890762,16.41442299,-28.34333038,16.20256042,-28.37516022,NA,0.0004954243195,0.000135446302,0.05590924621,164170.2344,2.731082439,0.4511356652,0.05289459229,0.3412810266,0.9998725057,0.403288424,0.126041159,"27676.55078;5134.108887;4891.382324;3844.573975;3443.866699;8253.693359;","27676.55078;5134.108887;4891.382324;3844.573975;3443.866699;8253.693359;","0.9022546411;0.816496551;0.816496551;0.816496551;0.8164966106;0.9730522037;",9531,0,2.108338833,0.0003001303994,164170.2344,0,0,606.8113403,"y5^1/644.3184814;y8^1/857.4298096;y10^1/999.5040283;y9^1/928.4669189;y6^1/715.3555908;b4-NH3^1/268.1291809;",131,0,0,0,0 +"G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\aleduc\miceotopes\Bulk\dAL_AT_Long_B1.raw","dAL_AT_Long_B1","Q6NZL0","Q6NZL0","SOGA3_MOUSE","Soga3",32284358,17883826,6782988.5,32284358,17883826,6782988.5,6183574.5,"AAAAAAAAQMHTK(SILAC-K-H)","AAAAAAAAQMHTK","AAAAAAAAQMHTK(SILAC-K-H)2",2,0.004283288959,0.1120364144,0.01398449857,0.0001518372301,0.000149097963,0.0001358142035,0.0001497678604,0,1,53441.0625,29856.25,45710.51172,NA,374572.2812,0.5068411231,15.01122189,14.77577591,15.24795341,-28.34333038,15.172966,-28.78292465,NA,0.0004954243195,0.000135446302,0.807780683,437919.875,2.389034748,0.2632122636,0.2098549008,0,0.8936085701,1.613744617,0.06964779645,"0;18378.38477;17024.44141;15426.27441;38014.78906;","0;18378.38477;17024.44141;15426.27441;38014.78906;","0;0.816496551;0.816496551;0.8164966106;0.3811839521;",8860,0,1.581254125,0.01099894103,0,437919.875,0,609.8214111,"y5^1/650.338623;y8^1/863.4499512;y9^1/934.4870605;y6^1/721.3757324;b4-NH3^1/268.1291809;",132,0,0,0,0 +"G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\aleduc\miceotopes\Bulk\dAL_AT_Long_B2.raw","dAL_AT_Long_B2","Q6NZL0","Q6NZL0","SOGA3_MOUSE","Soga3",44433220,14355674,6647798,44433220,14355674,6647798,6081964.5,"AAAAAAAAQMHTK(SILAC-K-H)","AAAAAAAAQMHTK","AAAAAAAAQMHTK(SILAC-K-H)2",2,0.006261997391,0.1597869694,0.01398449857,0.000157405957,0.0001544163097,0.0001358142035,0.0001551831228,0,1,79762.60938,26581.69531,64366.85547,NA,240023.2812,0.6600624323,14.51613331,14.28074741,14.7517662,-28.34333038,14.72296333,-28.85000229,NA,0.0004954243195,0.000135446302,0.807780683,297433.875,1.861950159,0.1426064521,0.2810209394,0,0.8532176018,1.194468856,0.07334788144,"12702.59766;0;0;8279.326172;58780.6875;","12702.59766;0;0;8279.326172;58780.6875;","0.816496551;0;0;0.8164966106;0.6042228341;",8572,0,1.054169416,0.01861365139,356748.7188,297433.875,0,609.8214111,"y5^1/650.338623;y8^1/863.4499512;y9^1/934.4870605;y6^1/721.3757324;b4-NH3^1/268.1291809;",132,0,0,0,0 +"G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\aleduc\miceotopes\Bulk\dAL_AT_Long_B8.raw","dAL_AT_Long_B8","Q6NZL0","Q6NZL0","SOGA3_MOUSE","Soga3",10869921,20067288,6876724.5,10869921,20067288,6876724.5,6176264.5,"AAAAAAAAQMHTK(SILAC-K-H)","AAAAAAAAQMHTK","AAAAAAAAQMHTK(SILAC-K-H)2",2,2.799317008e-05,0.0001256719988,0.01398449857,0.0001751006785,0.000171703301,0.0001358142035,0.0001723840687,0.8317982554,1,170265.7188,334150.1562,10442.45312,0.3308399916,0,0.924280107,16.25707817,16.01942253,16.41556931,-28.34333038,16.20256042,-28.20146179,NA,0.0004954243195,0.000135446302,0,0,1.06999743,0.05967807397,0.03326049075,0,0.1103457958,0.9151456952,0.0927252844,"9262.703125;0;0;0;161003.0156;","9262.703125;0;0;0;161003.0156;","0.6916281581;0;0;0;0.9376648664;",9580,0,1.066607237,0.231190756,164170.2344,0,0,609.8214111,"y5^1/650.338623;y8^1/863.4499512;y9^1/934.4870605;y6^1/721.3757324;b4-NH3^1/268.1291809;",132,0,0,0,0 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+"G:\.shortcut-targets-by-id\1uQ4exoKlaZAGnOG1iCJPzYN3ooYYZB7g\MS\Users\aleduc\miceotopes\Bulk\dAL_AT_Long_B5.raw","dAL_AT_Long_B5","Q14AX6","Q14AX6;Q8CCJ9","CDK12_MOUSE","Cdk12",142786.4531,193913.0625,220644.2188,142786.4531,193913.0625,220644.2188,NA,"AAAAAAAK(SILAC-K-L)","AAAAAAAK","AAAAAAAK(SILAC-K-L)1",1,0.008183306083,0.165974766,0.0004225292651,0.1369090527,0.03727342188,0.0001358142035,0.03709408268,0,0,142786.4531,193913.0625,141355.4531,NA,375019.8125,0.5432867408,8.87962532,8.640967369,9.117512703,-53.90829086,8.685803413,-53.1949501,NA,5.310815322e-05,0.000135446302,0.6113488078,378816.3125,2.330576897,0.445051223,0.03206285834,0,0.8521270752,2.209398746,0.5003484488,"130027.7891;9577.949219;9504.417969;2551.996826;3180.72583;1855.911743;0;0;0;","130027.7891;9577.949219;9504.417969;2551.996826;3180.72583;1855.911743;0;0;0;","0.5100164413;0.9473818541;0.9484211206;0;0.6865409613;0.2074242979;0;0;0;",5119,0.6370290518,1.472753882,6.412987568e-05,378816.3125,0,0,644.3726196,"b6^1/427.22995;b5^1/356.1928406;b7^1/498.2670593;y3^1/289.1870422;b4^1/285.1557312;y4^1/360.2241516;y6^1/502.2983704;y5^1/431.261261;b3^1/214.1186218;",179,0,0,0,0 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diff --git a/inst/tinytest/test_clean_DIANN.R b/inst/tinytest/test_clean_DIANN.R index 2f2a7ce1d..9c69fcd87 100644 --- a/inst/tinytest/test_clean_DIANN.R +++ b/inst/tinytest/test_clean_DIANN.R @@ -54,3 +54,25 @@ output <- MSstatsConvert:::.cleanRawDIANN(input, MBR = FALSE, qvalue_cutoff = 0. expect_qvalue_cutoff(output, "GlobalQValue", 0.001) output <- MSstatsConvert:::.cleanRawDIANN(input, MBR = FALSE, pg_qvalue_cutoff = 0.0002) expect_qvalue_cutoff(output, "GlobalPGQValue", 0.0002) + +# Test .assignDIANNIsotopeLabelType --------------------------- +# Channel path: Channel column is mapped to IsotopeLabelType, then dropped +dt_channel = data.table::data.table( + PeptideSequence = c("PEPTIDEK", "PEPTIDEK", "PEPTIDEK"), + Channel = c("H", "L", "other") +) +result_channel = MSstatsConvert:::.assignDIANNIsotopeLabelType( + dt_channel, labeledAminoAcids = c("K"), has_channel = TRUE +) +expect_equal(result_channel$IsotopeLabelType, c("H", "L", NA_character_)) +expect_false("Channel" %in% colnames(result_channel)) + +# NULL path: labeledAminoAcids = NULL returns input unchanged (no IsotopeLabelType added) +dt_null = data.table::data.table( + PeptideSequence = c("PEPTIDEK(SILAC-K-H)", "PEPTIDEK(SILAC-K-L)") +) +result_null = MSstatsConvert:::.assignDIANNIsotopeLabelType( + dt_null, labeledAminoAcids = NULL, has_channel = FALSE +) +expect_false("IsotopeLabelType" %in% colnames(result_null)) +expect_equal(nrow(result_null), 2L) diff --git a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R index 2cf5308e6..afc817439 100644 --- a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R +++ b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R @@ -1,3 +1,183 @@ +# Test DIANNtoMSstatsFormat SILAC protein turnover --------------------------- +# Dataset source: MSV000097050 +input_file_path_silac = system.file("tinytest/raw_data/DIANN/diann_input_silac.csv", + package = "MSstatsConvert") +annotation_file_path_silac = system.file("tinytest/raw_data/DIANN/annotation_silac.csv", + package = "MSstatsConvert") +input_silac = data.table::fread(input_file_path_silac) +annot_silac = data.table::fread(annotation_file_path_silac) +output_silac = DIANNtoMSstatsFormat(input_silac, annotation = annot_silac, + labeledAminoAcids = c("K"), + removeFewMeasurements = FALSE, + use_log_file = FALSE) +output_silac_dt = data.table::as.data.table(output_silac) + +# Basic structure +expect_equal(ncol(output_silac), 11) +expect_equal(nrow(output_silac), 1020) +expect_true("Run" %in% colnames(output_silac)) +expect_true("ProteinName" %in% colnames(output_silac)) +expect_true("PeptideSequence" %in% colnames(output_silac)) +expect_true("PrecursorCharge" %in% colnames(output_silac)) +expect_true("Intensity" %in% colnames(output_silac)) +expect_true("FragmentIon" %in% colnames(output_silac)) +expect_true("ProductCharge" %in% colnames(output_silac)) +expect_true("IsotopeLabelType" %in% colnames(output_silac)) +expect_true("Condition" %in% colnames(output_silac)) +expect_true("BioReplicate" %in% colnames(output_silac)) +expect_true("Fraction" %in% colnames(output_silac)) + +# IsotopeLabelType is classified as H/L/NA — not the "Light" default from +# the labeledAminoAcids=NULL path +expect_false("Light" %in% output_silac$IsotopeLabelType) +label_counts = table(output_silac$IsotopeLabelType, useNA = "ifany") +expect_equal(unname(label_counts["H"]), 350L) +expect_equal(unname(label_counts["L"]), 350L) +expect_equal(sum(is.na(output_silac$IsotopeLabelType)), 320L) + +# SILAC modification tags are stripped from PeptideSequence +expect_false(any(grepl("SILAC", output_silac$PeptideSequence))) + +# Peptides without a labeled K get NA IsotopeLabelType +unlabeled_rows = output_silac_dt[PeptideSequence %in% c("AAAAADLANR", "AAAADGEPLHNEEER")] +expect_true(all(is.na(unlabeled_rows$IsotopeLabelType))) + +# Peptides with a labeled K get only H or L +k_pep_rows = output_silac_dt[PeptideSequence %in% c("AAAAAAAAQMHTK", "AAAAAAAK", + "AAAAAAK", "AAAAAGGK")] +expect_true(all(k_pep_rows$IsotopeLabelType %in% c("H", "L"))) + +# Annotation merges correctly: run dAL_AT_Long_B1 maps to Condition 10 +cond_b1 = unique(output_silac_dt[Run == "dAL_AT_Long_B1", Condition]) +expect_equal(as.character(cond_b1), "10") + +# Heavy fragment intensities trace back to the heavy input rows. +# Input: AAAAAAAAQMHTK(SILAC-K-H), Run dAL_AT_Long_B1 has +# Fragment.Quant.Corrected = "0;18378.38477;17024.44141;15426.27441;38014.78906;" +# Fragment.Info ions (after NH3 removal): +# y8^1/863.4499512 -> 18378.38477, y9^1/934.4870605 -> 17024.44141, +# y6^1/721.3757324 -> 15426.27441 +heavy_b1 = output_silac_dt[PeptideSequence == "AAAAAAAAQMHTK" & + IsotopeLabelType == "H" & + Run == "dAL_AT_Long_B1"] +heavy_y8 = heavy_b1[FragmentIon == "y8^1/863.4499512", Intensity] +expect_equal(heavy_y8, 18378.38477, tolerance = 1) +heavy_y9 = heavy_b1[FragmentIon == "y9^1/934.4870605", Intensity] +expect_equal(heavy_y9, 17024.44141, tolerance = 1) +heavy_y6 = heavy_b1[FragmentIon == "y6^1/721.3757324", Intensity] +expect_equal(heavy_y6, 15426.27441, tolerance = 1) + +# Light fragment intensities trace back to the light input rows. +# Input: AAAAAAAAQMHTK(SILAC-K-L), Run dAL_AT_Long_B1 has +# Fragment.Quant.Corrected = "120170.8125;39879.93359;13874.50293;33449.03516;0;33788.10156;" +# Fragment.Info ions (after NH3 removal): +# y5^1/644.3184814 -> 120170.8125, y8^1/857.4298096 -> 39879.93359, +# y10^1/999.5040283 -> 13874.50293, y9^1/928.4669189 -> 33449.03516 +light_b1 = output_silac_dt[PeptideSequence == "AAAAAAAAQMHTK" & + IsotopeLabelType == "L" & + Run == "dAL_AT_Long_B1"] +light_y5 = light_b1[FragmentIon == "y5^1/644.3184814", Intensity] +expect_equal(light_y5, 120170.8125, tolerance = 1) +light_y8 = light_b1[FragmentIon == "y8^1/857.4298096", Intensity] +expect_equal(light_y8, 39879.93359, tolerance = 1) +light_y10 = light_b1[FragmentIon == "y10^1/999.5040283", Intensity] +expect_equal(light_y10, 13874.50293, tolerance = 1) +light_y9 = light_b1[FragmentIon == "y9^1/928.4669189", Intensity] +expect_equal(light_y9, 33449.03516, tolerance = 1) + +# Zero-intensity input fragments are converted to NA in output +# AAAAAAAAQMHTK(SILAC-K-L) B1 has y6^1/715.3555908 = 0 in input +light_y6_zero = light_b1[FragmentIon == "y6^1/715.3555908", Intensity] +expect_true(is.na(light_y6_zero)) + +# Verify cross-run consistency: B8 light intensities also trace to input +# Input: AAAAAAAAQMHTK(SILAC-K-L), Run dAL_AT_Long_B8 has +# Fragment.Quant.Corrected = "27676.55078;5134.108887;4891.382324;3844.573975;3443.866699;8253.693359;" +light_b8 = output_silac_dt[PeptideSequence == "AAAAAAAAQMHTK" & + IsotopeLabelType == "L" & + Run == "dAL_AT_Long_B8"] +light_y5_b8 = light_b8[FragmentIon == "y5^1/644.3184814", Intensity] +expect_equal(light_y5_b8, 27676.55078, tolerance = 1) +light_y8_b8 = light_b8[FragmentIon == "y8^1/857.4298096", Intensity] +expect_equal(light_y8_b8, 5134.108887, tolerance = 1) + +# Test DIANNtoMSstatsFormat PXD055942 (DIANN 2.0 + Channel-based SILAC) ------ +# Dataset: PXD055942 (heart protein turnover, 0/8/32 day timepoints). +# Uses quantificationColumn = "auto" (Fr.N.Quantity columns) and the Channel +# column path for IsotopeLabelType (no SILAC suffix in ModifiedSequence). +input_file_path_pxd = system.file("tinytest/raw_data/DIANN/PXD055942.parquet", + package = "MSstatsConvert") +annotation_file_path_pxd = system.file("tinytest/raw_data/DIANN/annotation_PXD055942.csv", + package = "MSstatsConvert") +input_pxd = arrow::read_parquet(input_file_path_pxd) +annot_pxd = data.table::fread(annotation_file_path_pxd) +output_pxd = DIANNtoMSstatsFormat(input_pxd, annotation = annot_pxd, + labeledAminoAcids = c("K"), + removeFewMeasurements = FALSE, + quantificationColumn = "auto", + use_log_file = FALSE) +output_pxd_dt = data.table::as.data.table(output_pxd) + +# Basic structure +expect_equal(ncol(output_pxd), 11) +expect_equal(nrow(output_pxd), 20400) +expect_true("Run" %in% colnames(output_pxd)) +expect_true("ProteinName" %in% colnames(output_pxd)) +expect_true("PeptideSequence" %in% colnames(output_pxd)) +expect_true("PrecursorCharge" %in% colnames(output_pxd)) +expect_true("Intensity" %in% colnames(output_pxd)) +expect_true("FragmentIon" %in% colnames(output_pxd)) +expect_true("ProductCharge" %in% colnames(output_pxd)) +expect_true("IsotopeLabelType" %in% colnames(output_pxd)) +expect_true("Condition" %in% colnames(output_pxd)) +expect_true("BioReplicate" %in% colnames(output_pxd)) +expect_true("Fraction" %in% colnames(output_pxd)) + +# Channel path used: H/L/NA counts, no "Light" default +expect_false("Light" %in% output_pxd$IsotopeLabelType) +pxd_label_counts = table(output_pxd$IsotopeLabelType, useNA = "ifany") +expect_equal(unname(pxd_label_counts["H"]), 8712L) +expect_equal(unname(pxd_label_counts["L"]), 8712L) +expect_equal(sum(is.na(output_pxd$IsotopeLabelType)), 2976L) + +# Channel path does NOT strip (SILAC) from PeptideSequence — that notation is +# part of the peptide identity in this format, not a label indicator +expect_true(any(grepl("(SILAC)", output_pxd$PeptideSequence, fixed = TRUE))) + +# Unlabeled peptides (no K, no SILAC) get NA IsotopeLabelType +pxd_unlabeled = output_pxd_dt[PeptideSequence %in% c("AVLEEAEFQR", "DDEGLYTLR", + "DTELAEELLQWFLQEEK")] +expect_true(all(is.na(pxd_unlabeled$IsotopeLabelType))) + +# Annotation maps correctly to all three timepoint conditions +expect_true("0 day" %in% output_pxd$Condition) +expect_true("8 days" %in% output_pxd$Condition) +expect_true("32 days" %in% output_pxd$Condition) +run_0d = "20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_0d_1" +expect_equal(as.character(unique(output_pxd_dt[Run == run_0d, Condition])), "0 day") + +# Heavy fragment intensities match Fr.N.Quantity from the Channel = "H" input row. +# Input: AFMTADLPNELIELLEK(SILAC)(SILAC)(SILAC), Run 32d_1, Channel H has +# Fr.0.Quantity = 662450.1 (largest fragment — should be the max output intensity) +h_pxd_pep = "AFMTADLPNELIELLEK(SILAC)(SILAC)(SILAC)" +h_pxd_run = "20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_32d_1" +h_pxd_ints = output_pxd_dt[PeptideSequence == h_pxd_pep & + IsotopeLabelType == "H" & + Run == h_pxd_run, Intensity] +expect_equal(max(h_pxd_ints, na.rm = TRUE), 662450.1, tolerance = 1) + +# Light fragment intensities match Fr.N.Quantity from the Channel = "L" input row. +# Input: APVYSGSSPVSGYFVDFK(SILAC)(SILAC)(SILAC)EEDSGEWK(SILAC)(SILAC)(SILAC), +# Run 32d_2, Channel L has Fr.1.Quantity = 116961.9 (largest fragment) +l_pxd_pep = "APVYSGSSPVSGYFVDFK(SILAC)(SILAC)(SILAC)EEDSGEWK(SILAC)(SILAC)(SILAC)" +l_pxd_run = "20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_32d_2" +l_pxd_ints = output_pxd_dt[PeptideSequence == l_pxd_pep & + IsotopeLabelType == "L" & + Run == l_pxd_run, Intensity] +expect_equal(max(l_pxd_ints, na.rm = TRUE), 116961.9, tolerance = 1) +# Fr.0.Quantity = 4973.411 also appears in the output +expect_true(any(abs(l_pxd_ints - 4973.411) < 1, na.rm = TRUE)) + # Test DIANNtoMSstatsFormat --------------------------- input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", package="MSstatsConvert") annotation_file_path = system.file("tinytest/raw_data/DIANN/annotation.csv", package = "MSstatsConvert") @@ -17,6 +197,8 @@ expect_true("IsotopeLabelType" %in% colnames(output)) expect_true("Condition" %in% colnames(output)) expect_true("BioReplicate" %in% colnames(output)) expect_true("Fraction" %in% colnames(output)) +# When labeledAminoAcids = NULL (default), IsotopeLabelType is filled with "Light" +expect_true(all(output$IsotopeLabelType == "Light")) # Test DIANNtoMSstatsFormat DIANN 2.0 ------------------------ input_file_path = system.file("tinytest/raw_data/DIANN/diann_2.0.parquet", package="MSstatsConvert") @@ -36,4 +218,6 @@ expect_true("ProductCharge" %in% colnames(output)) expect_true("IsotopeLabelType" %in% colnames(output)) expect_true("Condition" %in% colnames(output)) expect_true("BioReplicate" %in% colnames(output)) -expect_true("Fraction" %in% colnames(output)) \ No newline at end of file +expect_true("Fraction" %in% colnames(output)) +# When labeledAminoAcids = NULL (default), IsotopeLabelType is filled with "Light" +expect_true(all(output$IsotopeLabelType == "Light")) \ No newline at end of file diff --git a/inst/tinytest/test_feature_cleaning.R b/inst/tinytest/test_utils_clean_features.R similarity index 89% rename from inst/tinytest/test_feature_cleaning.R rename to inst/tinytest/test_utils_clean_features.R index a3d0c6ccc..aec83c3fe 100644 --- a/inst/tinytest/test_feature_cleaning.R +++ b/inst/tinytest/test_utils_clean_features.R @@ -187,6 +187,35 @@ expect_equal( data.table::setkey(to_filter_channel2[!(ProteinName == "B"), ], NULL) ) +# Test .classifyIsotopeLabelType ---- +# DIANN mode: explicit SILAC-H / SILAC-L suffix tags +dt_diann = data.table::data.table(PeptideSequence = c( + "PEPTIDEK(SILAC-K-H)", # heavy + "PEPTIDEK(SILAC-K-L)", # light + "PEPTIDEAC" # neither -> NA +)) +result_diann = MSstatsConvert:::.classifyIsotopeLabelType( + dt_diann, + heavy_regex = "\\(SILAC-(?:K)-H\\)", + light_regex = "\\(SILAC-(?:K)-L\\)" +) +expect_equal(result_diann$IsotopeLabelType, c("H", "L", NA_character_)) + +# DIANN mode with multiple labeled amino acids (K and R) +dt_multi = data.table::data.table(PeptideSequence = c( + "PEPTIDEK(SILAC-K-H)", # heavy K + "PEPTIDER(SILAC-R-H)", # heavy R + "PEPTIDEK(SILAC-K-L)", # light K + "PEPTIDER(SILAC-R-L)", # light R + "PEPTIDEAC" # NA +)) +result_multi = MSstatsConvert:::.classifyIsotopeLabelType( + dt_multi, + heavy_regex = "\\(SILAC-(?:K|R)-H\\)", + light_regex = "\\(SILAC-(?:K|R)-L\\)" +) +expect_equal(result_multi$IsotopeLabelType, c("H", "H", "L", "L", NA_character_)) + # Utility function ---- expect_equal(MSstatsConvert:::.combine(c("A", "B"), c("A", "B")), c("A_A", "B_B")) diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd index 24cdc0598..e89f9cdbb 100644 --- a/man/DIANNtoMSstatsFormat.Rd +++ b/man/DIANNtoMSstatsFormat.Rd @@ -15,6 +15,7 @@ DIANNtoMSstatsFormat( removeOxidationMpeptides = TRUE, removeProtein_with1Feature = TRUE, MBR = TRUE, + labeledAminoAcids = NULL, quantificationColumn = "FragmentQuantCorrected", calculateAnomalyScores = FALSE, anomalyModelFeatures = c(), @@ -61,6 +62,32 @@ the library created after the first MBR pass. Default is 0.01.} \item{MBR}{True if analysis was done with match between runs} +\item{labeledAminoAcids}{Character vector of single-letter amino acid codes +that carry the SILAC label in protein turnover experiments, e.g. +\code{c("K")} or \code{c("K", "R")}. Supplying this vector opts in to +protein-turnover mode; the exact amino acids determine behaviour only in the +\code{ModifiedSequence}-parsing path described below. + +\strong{Channel-based path} (DIA-NN 2.x exports that include a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +\emph{and} the input contains a \code{Channel} column, \code{Channel} values +are mapped directly to \code{IsotopeLabelType} (\code{"H"} → \code{"H"}, +\code{"L"} → \code{"L"}, anything else → \code{NA}). The amino acid codes +in \code{labeledAminoAcids} are \strong{not} used to validate or filter +\code{ModifiedSequence} in this path. + +\strong{ModifiedSequence-parsing path} (DIA-NN 1.x exports without a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +and no \code{Channel} column is present, each \code{ModifiedSequence} is +inspected for SILAC suffixes of the form \code{(SILAC--H)} or +\code{(SILAC--L)}, where \code{} is one of the supplied amino acid +codes. Matching sequences are classified as \code{"H"} or \code{"L"}; +sequences carrying neither suffix receive \code{IsotopeLabelType = NA}. +The SILAC suffix is then stripped from \code{PeptideSequence}. + +When \code{NULL} (default), protein-turnover mode is disabled and all +peptides receive \code{IsotopeLabelType = "Light"}.} + \item{quantificationColumn}{Use 'FragmentQuantCorrected'(default) column for quantified intensities for DIANN 1.8.x. Use 'FragmentQuantRaw' for quantified intensities for DIANN 1.9.x. Use 'auto' for quantified intensities for DIANN 2.x where each fragment intensity is a separate column, e.g. Fr0Quantity.} diff --git a/man/MSstatsClean.Rd b/man/MSstatsClean.Rd index 3a7e896fe..d5559610b 100644 --- a/man/MSstatsClean.Rd +++ b/man/MSstatsClean.Rd @@ -73,7 +73,8 @@ MSstatsClean(msstats_object, ...) qvalue_cutoff = 0.01, pg_qvalue_cutoff = 0.01, calculateAnomalyScores = FALSE, - anomalyModelFeatures = c() + anomalyModelFeatures = c(), + labeledAminoAcids = NULL ) \S4method{MSstatsClean}{MSstatsMetamorpheusFiles}(msstats_object, MBR = TRUE, qvalue_cutoff = 0.05) @@ -170,6 +171,32 @@ Default is 0.01.} column, i.e. the global q-value for the protein group. If MBR is true, the qvalue cutoff for the Lib.PG.Q.Value column, i.e. the protein group q-value for the library created after the first MBR pass. Default is 0.01.} + +\item{labeledAminoAcids}{Character vector of single-letter amino acid codes +that carry the SILAC label in protein turnover experiments, e.g. +\code{c("K")} or \code{c("K", "R")}. Supplying this vector opts in to +protein-turnover mode; the exact amino acids determine behaviour only in the +\code{ModifiedSequence}-parsing path described below. + +\strong{Channel-based path} (DIA-NN 2.x exports that include a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +\emph{and} the input contains a \code{Channel} column, \code{Channel} values +are mapped directly to \code{IsotopeLabelType} (\code{"H"} → \code{"H"}, +\code{"L"} → \code{"L"}, anything else → \code{NA}). The amino acid codes +in \code{labeledAminoAcids} are \strong{not} used to validate or filter +\code{ModifiedSequence} in this path. + +\strong{ModifiedSequence-parsing path} (DIA-NN 1.x exports without a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +and no \code{Channel} column is present, each \code{ModifiedSequence} is +inspected for SILAC suffixes of the form \code{(SILAC--H)} or +\code{(SILAC--L)}, where \code{} is one of the supplied amino acid +codes. Matching sequences are classified as \code{"H"} or \code{"L"}; +sequences carrying neither suffix receive \code{IsotopeLabelType = NA}. +The SILAC suffix is then stripped from \code{PeptideSequence}. + +When \code{NULL} (default), protein-turnover mode is disabled and all +peptides receive \code{IsotopeLabelType = "Light"}.} } \value{ data.table diff --git a/man/dot-cleanRawDIANN.Rd b/man/dot-cleanRawDIANN.Rd index 51af8bc28..da61ebc1c 100644 --- a/man/dot-cleanRawDIANN.Rd +++ b/man/dot-cleanRawDIANN.Rd @@ -12,7 +12,8 @@ qvalue_cutoff = 0.01, pg_qvalue_cutoff = 0.01, calculateAnomalyScores = FALSE, - anomalyModelFeatures = c() + anomalyModelFeatures = c(), + labeledAminoAcids = NULL ) } \arguments{ @@ -40,6 +41,32 @@ the library created after the first MBR pass. Default is 0.01.} \item{calculateAnomalyScores}{Default is FALSE. If TRUE, will run anomaly detection model and calculate anomaly scores for each feature. Used downstream to weigh measurements in differential analysis.} \item{anomalyModelFeatures}{character vector of quality metric column names to be used as features in the anomaly detection model. List must not be empty if calculateAnomalyScores=TRUE.} + +\item{labeledAminoAcids}{Character vector of single-letter amino acid codes +that carry the SILAC label in protein turnover experiments, e.g. +\code{c("K")} or \code{c("K", "R")}. Supplying this vector opts in to +protein-turnover mode; the exact amino acids determine behaviour only in the +\code{ModifiedSequence}-parsing path described below. + +\strong{Channel-based path} (DIA-NN 2.x exports that include a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +\emph{and} the input contains a \code{Channel} column, \code{Channel} values +are mapped directly to \code{IsotopeLabelType} (\code{"H"} → \code{"H"}, +\code{"L"} → \code{"L"}, anything else → \code{NA}). The amino acid codes +in \code{labeledAminoAcids} are \strong{not} used to validate or filter +\code{ModifiedSequence} in this path. + +\strong{ModifiedSequence-parsing path} (DIA-NN 1.x exports without a +\code{Channel} column): when \code{labeledAminoAcids} is non-\code{NULL} +and no \code{Channel} column is present, each \code{ModifiedSequence} is +inspected for SILAC suffixes of the form \code{(SILAC--H)} or +\code{(SILAC--L)}, where \code{} is one of the supplied amino acid +codes. Matching sequences are classified as \code{"H"} or \code{"L"}; +sequences carrying neither suffix receive \code{IsotopeLabelType = NA}. +The SILAC suffix is then stripped from \code{PeptideSequence}. + +When \code{NULL} (default), protein-turnover mode is disabled and all +peptides receive \code{IsotopeLabelType = "Light"}.} } \value{ data.table