Description Usage Arguments Value Examples
Takes a ThermoFisher MSF file and finds the location of each peptide within its corresponding protein sequence. In cases where a single peptide maps to multiple locations within a protein sequence, only the first location is reported. If a peptide maps ambiguously to multiple proteins, all locations are reported with data from each peptide-protein combination on a separate row.
1 | map_peptides(msf_file, min_conf = "High", prot_regex = "")
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msf_file |
A file path to a ThermoFisher MSF file. |
min_conf |
"High", "Medium", or "Low". The minimum peptide confidence level to retrieve from MSF file. |
prot_regex |
Regular expression where the first group matches a protein name or ID from the protein description. Regex must contain ONE group. The protein description is typically generated from a fasta reference file that was used for the database search. |
A dataframe containing start and stop positions (relative to the parent protein sequence) for each peptide in the database.
peptide_id |
a unique peptide ID |
spectrum_id |
a unique spectrum ID |
protein_id |
unique protein group ID to which this peptide maps |
protein_desc |
protein description from reference database used to assign peptides to protein groups, parsed according to |
peptide_sequence |
amino acid sequence (does not show post-translational modifications) |
pep_score |
PEP score |
q_value |
Q-value score |
protein_sequence |
parent protein sequence |
start |
start position of peptide within protein sequence |
end |
end position of peptide within protein sequence |
1 | map_peptides(parsemsf_example("test_db.msf"))
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