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Import Metamorpheus files into PTM format

Source: R/converters.R
MetamorpheusToMSstatsPTMFormat.Rd

Import Metamorpheus files into PTM format

Usage

MetamorpheusToMSstatsPTMFormat(
  input,
  annotation,
  fasta_path,
  input_protein = NULL,
  annotation_protein = NULL,
  use_unmod_peptides = FALSE,
  mod_ids = c("\\[Common Biological:Phosphorylation on S\\]"),
  useUniquePeptide = TRUE,
  removeFewMeasurements = TRUE,
  removeProtein_with1Feature = FALSE,
  summaryforMultipleRows = max,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL
)

Arguments

input

name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output.

annotation

name of 'annotation.txt' data which includes Condition, BioReplicate.

fasta_path

string containing path to the corresponding fasta file for the modified peptide dataset.

input_protein

same as input for global profiling run. Default is NULL.

annotation_protein

same as annotation for global profiling run. Default is NULL.

use_unmod_peptides

If protein_input is not provided, unmodified peptides can be extracted from input to be used in place of a global profiling run. Default is FALSE.

mod_ids

List of modifications of interest. Default is a list with only Common Biological:Phosphorylation on S. Please note that the 'mod_ids' parameter currently supports lists of size 1 only. Future updates aim to extend its functionality to accommodate lists of greater sizes. Note \\ must be included before special characters.

useUniquePeptide

TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.

removeFewMeasurements

TRUE (default) will remove the features that have 1 or 2 measurements across runs.

removeProtein_with1Feature

TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.

summaryforMultipleRows

max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.

use_log_file

logical. If TRUE, information about data processing will be saved to a file.

append

logical. If TRUE, information about data processing will be added to an existing log file.

verbose

logical. If TRUE, information about data processing wil be printed to the console.

log_file_path

character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.

Value

a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.

Author

Anthony Wu

Examples

input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", 
                                package = "MSstatsPTM")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv", 
                                package = "MSstatsPTM")
annot = data.table::fread(annot)
input_protein = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv",
                                package = "MSstatsPTM")
input_protein = data.table::fread(input_protein)
annot_protein = system.file("tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv", 
                                package = "MSstatsPTM")
annot_protein = data.table::fread(annot_protein)
fasta_path=system.file("extdata", "metamorpheus_fasta.fasta", 
                                package="MSstatsPTM")
metamorpheus_imported = MetamorpheusToMSstatsPTMFormat(
    input, 
    annot, 
    fasta_path=fasta_path,
    input_protein=input_protein,
    annotation_protein=annot_protein,
    use_unmod_peptides=FALSE,
    mod_ids = c("\\[Common Fixed:Carbamidomethyl on C\\]")
)
#> [1] "FASTA file missing 3 Proteins. These will be removed. This may be due to non-unique identifications."
#> INFO  [2026-04-09 15:19:19] ** Raw data from Metamorpheus imported successfully.
#> INFO  [2026-04-09 15:19:19] ** Raw data from Metamorpheus cleaned successfully.
#> INFO  [2026-04-09 15:19:19] ** Using provided annotation.
#> INFO  [2026-04-09 15:19:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
#> INFO  [2026-04-09 15:19:19] ** The following options are used:
#>   - Features will be defined by the columns: PeptideSequence, PrecursorCharge
#>   - Shared peptides will be removed.
#>   - Proteins with single feature will not be removed.
#>   - Features with less than 3 measurements across runs will be removed.
#> INFO  [2026-04-09 15:19:19] ** Features with all missing measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Shared peptides are removed.
#> INFO  [2026-04-09 15:19:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
#> INFO  [2026-04-09 15:19:19] ** Features with one or two measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Run annotation merged with quantification data.
#> INFO  [2026-04-09 15:19:19] ** Features with one or two measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Fractionation handled.
#> INFO  [2026-04-09 15:19:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
#> INFO  [2026-04-09 15:19:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
#> INFO  [2026-04-09 15:19:19] ** Raw data from Metamorpheus imported successfully.
#> INFO  [2026-04-09 15:19:19] ** Raw data from Metamorpheus cleaned successfully.
#> INFO  [2026-04-09 15:19:19] ** Using provided annotation.
#> INFO  [2026-04-09 15:19:19] ** Run labels were standardized to remove symbols such as '.' or '%'.
#> INFO  [2026-04-09 15:19:19] ** The following options are used:
#>   - Features will be defined by the columns: PeptideSequence, PrecursorCharge
#>   - Shared peptides will be removed.
#>   - Proteins with single feature will not be removed.
#>   - Features with less than 3 measurements across runs will be removed.
#> INFO  [2026-04-09 15:19:19] ** Features with all missing measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Shared peptides are removed.
#> INFO  [2026-04-09 15:19:19] ** Multiple measurements in a feature and a run are summarized by summaryforMultipleRows: max
#> INFO  [2026-04-09 15:19:19] ** Features with one or two measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Run annotation merged with quantification data.
#> INFO  [2026-04-09 15:19:19] ** Features with one or two measurements across runs are removed.
#> INFO  [2026-04-09 15:19:19] ** Fractionation handled.
#> INFO  [2026-04-09 15:19:19] ** Updated quantification data to make balanced design. Missing values are marked by NA
#> INFO  [2026-04-09 15:19:19] ** Finished preprocessing. The dataset is ready to be processed by the dataProcess function.
head(metamorpheus_imported$PTM)
#>   ProteinName
#> 1 P06748_C104
#> 2 P06748_C104
#> 3 P06748_C104
#> 4 P06748_C104
#> 5 P06748_C104
#> 6 P06748_C104
#>                                                                                  PeptideSequence
#> 1 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#> 2 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#> 3 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#> 4 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#> 5 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#> 6 C[Common Fixed:Carbamidomethyl on C]GSGPVHISGQHLVAVEEDAES[UniProt:Phosphoserine on S]EDEEEEDVK
#>   PrecursorCharge FragmentIon ProductCharge IsotopeLabelType Condition
#> 1               3          NA            NA                L   control
#> 2               3          NA            NA                L   control
#> 3               3          NA            NA                L     1_min
#> 4               3          NA            NA                L     1_min
#> 5               3          NA            NA                L    10_min
#> 6               3          NA            NA                L    10_min
#>   BioReplicate                                                   Run Fraction
#> 1            1    180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib        1
#> 2            2    180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib        1
#> 3            3  180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib        1
#> 4            4  180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib        1
#> 5            5 180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib        1
#> 6            6 180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib        1
#>   Intensity
#> 1  224148.4
#> 2        NA
#> 3        NA
#> 4  251253.7
#> 5  188734.7
#> 6        NA
head(metamorpheus_imported$PROTEIN)
#>        ProteinName                                PeptideSequence
#> 1 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#> 2 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#> 3 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#> 4 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#> 5 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#> 6 Q8N3V7;UNDEFINED AAS[UniProt:Phosphoserine on S]PAKPSSLDLVPNLPK
#>   PrecursorCharge FragmentIon ProductCharge IsotopeLabelType Condition
#> 1               3          NA            NA                L   control
#> 2               3          NA            NA                L   control
#> 3               3          NA            NA                L     1_min
#> 4               3          NA            NA                L     1_min
#> 5               3          NA            NA                L    10_min
#> 6               3          NA            NA                L    10_min
#>   BioReplicate                                                   Run Fraction
#> 1            7    180323acs_001_HUVEC_P5_no_VEGF_control_1_001-calib        1
#> 2            8    180323acs_002_HUVEC_P5_no_VEGF_control_1_002-calib        1
#> 3            9  180323acs_003_HUVEC_P5_50ng_mL_VEGF_1min_1_001-calib        1
#> 4           10  180323acs_004_HUVEC_P5_50ng_mL_VEGF_1min_1_002-calib        1
#> 5           11 180323acs_007_HUVEC_P5_50ng_mL_VEGF_10min_1_001-calib        1
#> 6           12 180323acs_008_HUVEC_P5_50ng_mL_VEGF_10min_1_002-calib        1
#>   Intensity
#> 1  602295.6
#> 2  572816.1
#> 3  815920.8
#> 4  856970.5
#> 5  776769.5
#> 6  853108.7