| calculate_all_Area | Calculate Area/Intensity for the whole input sequence dataframe | 
| calculate_all_PSM | Calculate Spectra Count (PSM) for the whole input sequence dataframe | 
| calculate_Area | Calculate Area/Intensity for one row of the input sequence dataframe | 
| calculate_PSM | Calculate Spectra Count (PSM) for one row of the input sequence dataframe | 
| combine_files_from_folder | Combine CSV and TXT Files from a Folder | 
| convert_to_regex_pattern | Convert Peptide Sequence to Regex Pattern | 
| create_peptide_plot | Create a peptide Plot | 
| match_and_calculate_positions | Match peptide sequence with provided sequence and calculate positions | 
| obtain_mod | Obtain post translational modification(PTM) information from Peptide data based on the specified data type | 
| obtain_mod_Comet | Obtain modification information from Peptide data generated by Comet | 
| obtain_mod_DIANN | Obtain modification information from Peptide data generated by DIA-NN | 
| obtain_mod_Maxquant | Obtain modification information from Peptide data generated by Maxquant | 
| obtain_mod_MSFragger | Obtain modification information from Peptide data generated by MSFragger | 
| obtain_mod_mzIdenML | Obtain modification information from Peptide data generated by mzIdenML | 
| obtain_mod_mzTab | Obtain modification information from Peptide data generated by mzTab | 
| obtain_mod_PEAKS | Obtain modification information from Peptide data generated by PEAKS | 
| obtain_mod_Skyline | Obtain modification information from Peptide data generated by Skyline | 
| obtain_mod_Spectronaut | Obtain modification information from Peptide data generated by Spectronaut | 
| peptide_quantification | Peptide Quantification | 
| run_pepmap_app | Launch PepMapViz Shiny Application | 
| strip_sequence | Strip peptide sequences based on the specified data type | 
| strip_sequence_Comet | Strip sequence from Comet outputs | 
| strip_sequence_DIANN | Strip sequence from DIANN outputs | 
| strip_sequence_Maxquant | Strip sequence from Maxquant outputs | 
| strip_sequence_MSFragger | Strip sequence from MSFragger outputs | 
| strip_sequence_PEAKS | Strip sequence from PEAKS outputs | 
| strip_sequence_Skyline | Strip sequence from Skyline outputs | 
| strip_sequence_Spectronaut | Strip sequence from Spectronaut outputs |