Welcome to the Protein Contaminants Repository of the Max Perutz Labs MS Facility. In mass spectrometry experiments, it's crucial to account for potential contaminants that may interfere with accurate protein identification. This repository is dedicated to managing and versioning our custom FASTA contaminants file that we use in our facility service.
To ensure compatibility with a wide range of bioinformatics software, the contaminants FASTA file should only contain UniProtKB entries or entries have to adhere to the UniProtKB format, which is outlined in detail on uniprot.org.
The UniProtKB format is specified as follows:
>db|UniqueIdentifier|EntryName ProteinName OS=OrganismName OX=OrganismIdentifier GN=GeneName PE=ProteinExistence SV=SequenceVersion
For custom protein entries not present in the UniProt database, such as protein tags, engineered proteins, or synthetic constructs, a specific convention is followed. The db field is set as "xx," OrganismName is designated as "Synthetic," and OrganismIdentifier is specified as "0000." Moreover, special care should be taken to ensure that the UniqueIdentifier does not overlap with any existing UniProt Accession number.
- /archive: This directory contains previous versions of the contaminants file.
- contaminants_YYYY_NN.fasta: The main contaminants file used in current projects of the MS facility. The file is named according to the convention
contaminants_YEAR_NUMBER.fasta, where YEAR represents the current year, and NUMBER is a running index with two digits reset to 1 each year. The UniProtUniqueIdentifiersof FASTA entries are prefixed with contam_ to indicate that they originate from a contaminants FASTA file.- For example,
>sp|P13646|K1C13_HUMANbecomes>sp|contam_P13646|K1C13_HUMAN.
- For example,
- contaminants_notag_YYYY_NN.fasta: Identical to the main contaminants file, with the sole distinction that the
UniqueIdentifierof each entry is not prefixed with the contam_ tag.
For a detailed list of changes made to the contaminants FASTA file in each release, please refer to the CHANGELOG.md file.
If you have any questions or inquiries regarding this repository, please feel free to reach out to Markus Hartl at the Mass Spectrometry Facility of the Max Perutz Labs.
This repository is licensed under the MIT License