# Import

# Introduction

This vignette gives an overview about importing files for downstream analysis with mpwR.

## Import

Importing the output files from each software can be easily performed with `prepare_mpwR`. Please put all output files in one folder and follow the guidelines for naming the files. No other files/subfolders are allowed.

    files <- prepare_mpwR(path = "Path_to_Folder_with_files")

## Naming Files

The software output files need to be named according some simple rules.

### Suffix

Please use the following suffixes for the corresponding software:

- Spectronaut
  - *.tsv - _Report
- MaxQuant
  - evidence.txt - _evidence
  - peptides.txt - _peptides
  - proteinGroups.txt - _proteinGroups
- DIA-NN
  - *.tsv - _Report
- ProteomeDiscoverer
  - PSMs.txt - _PSMs
  - PeptideGroups.txt - _PeptideGroups
  - Proteins.txt - _Proteins
  - ProteinGroups.txt - _ProteinGroups

Note that the suffixes for MaxQuant and ProteomeDiscoverer can be used as is.

### Prefix

Please use the same prefix for your analysis and the respective software output file(s). Each analysis needs a unique identifier.

Examples:

- Spectronaut
  - WorkflowA1_Report.tsv
- MaxQuant
  - WorkflowA2_evidence.txt
  - WorkflowA2_peptide.txt
  - WorkflowA2_proteinGroups.txt
- DIA-NN
  - WorkflowA3_Report.tsv
- ProteomeDiscoverer
  - WorkflowA4_PSMs.txt
  - WorkflowA4_PeptideGroups.txt
  - WorkflowA4_Proteins.txt
  - WorkflowA4_ProteinGroups.txt

## Handling Error Messages

Subsequently, common error messages are explained and solutions are pointed out.

### Wrong suffix

Error in prepare_mpwR(path = path) : Unknown file suffix detected! Please use: _evidence, _peptides, _proteinGroups, _PSMs, _Proteins, _PeptideGroups, _ProteinGroups, _Report

Solution: Check your suffixes and make sure to use the correct spelling and the correct one for the respective software.

### Wrong number of files

Error in prepare_mpwR(path = path) : Wrong number of analyses detected for WorkflowA2! MaxQuant requires 3 input files. Remember: Use unique name for each analysis.

Solution: Make sure to include all output files from the respective software. MaxQuant requires 3 files, PD 4 files, DIA-NN and Spectronaut 1 file, respectively. Also use the same name (prefix) for all files.

### Subfolder

Error in data.table::fread(input_file, …) : File ‘DIR//subfolder’ is a directory. Not yet implemented.

Solution: Do not use subfolders in the directory of the output files. Put all files in a folder and use this path for prepare_mpwR.

### Same file name

Error in prepare_mpwR(path = path) : Please use a unique filename for each analysis.

Solution: Please use a unique name (prefix) for each respective output file(s). E.g. if you used…:

- WorkflowA1_Report.tsv
- WorkflowA1_evidence.txt
- WorkflowA1_peptide.txt
- WorkflowA1_proteinGroups.txt

… the error message is displayed. As a solution, for example add the used software to the name:

- WorkflowA1_Spectronaut_Report.tsv
- WorkflowA1_MQ_evidence.txt
- WorkflowA1_MQ_peptide.txt
- WorkflowA1_MQ_proteinGroups.txt

### Missing columns

Error in prepare_input(ordered_files[[i]][[“data”]][[“DIA-NN”]], software = “DIA-NN”) : Not all required columns present in submitted data.

Here example for DIA-NN. Similar messages for other software tools. Please make sure to include all required columns for the used software. Details are in the vignette Requirements.