MS2Ladder, v1.0.1

MS2Ladder This is a command-line script working in an R environment to validate amino acid residues obtained by shotgun proteomics. When reconstructing protein sequences from shotgun proteomics data, this script can be used to replace amino acid residues not supported by tandem mass spectra with "X". In other words, it performs the "building ladders" operation on MS2 spectra computationally, using the output text files from MaxQuant software. Overview This R script first takes MaxQuant's "msms.txt" file as input and, for each PSM, replaces amino acid residues that are not supported by MS2 spectra with "X". Next, using MaxQuant's "peptides.txt" file as a reference, it processes each peptide sequence by retaining only those amino acid residues supported by MS2, replacing unsupported residues with "X". It then returns the validated peptide sequences as an output. Usage Steps Move the subject "msms.txt" and "peptides.txt" files (e.g., msms_PF02B2_CID_60k.txt and peptides_PF02B2_CID_60k.txt) to a specific directory. Modify file paths for the input files and output directory in the sequence_ladder.R file. Execute the sequence_ladder.R script in R environment. The validated PSM sequences are obtained as a supportedmsms.txt file. Move the resultant "supportedmsms.txt" file (e.g., supportedmsms_PF02B2_CID_60k.txt) to a specific directory. Modify file paths for the input files and output directory in the integrate_peptides_msms.R file. Execute the integrate_peptides_msms.R script in R environment. The validated and merged peptide sequences are obtained as a "checkedpeptides.txt" file. Example of input files msms_PF02B2_CID_60k.txt: MaxQunat "msms.txt" file generated in an analysis of a fossil mandible of a Pleistocene Sus specimen from Penghu Channel, Taiwan. Please see Tsutaya et al. 2025 (Science 388:176–180) for the details of this file. Output files supportedmsms.txt: Text file derived from the input "msms.txt" file. The column names have been normalized, and the results of the sequence_ladder.R script have been appended. PSM sequences in which amino acid residues not supported by MS2 spectra have been replaced with "X" are stored in the $supported_residues column. To aid visual understanding, the "ladder" is stored in the $support_map column. checkedpeptides.txt: Text file derived from the input "peptides.txt" file. The column names have been normalized, and the results of the integrate_peptides_msms.R script have been appended.Peptide sequences consisting only of amino acid residues supported in the corresponding PSMs, with unsupported residues replaced by "X", are stored in the `$sequence_checked` column. Credits Yumeko Tarusawa and Takumi Tsutaya Citation If applicable, please cite the released version of this script, uploaded to Zenodo with a persistent identifier. License This project is licensed under the MIT License.