database

The Database command can be used to prepare a protein FASTA file for the following analysis. The database can be downloaded using the UniProt Proteome ID or by using a pre-formed FASTA file.

Usage

philosopher database [flags]

Flags

--add

Allows you to add one or more custom sequences to your database. Only UniProt FASTA formatting is allowed.

--annotate

Process a ready-to-use database.

--contam

Add 116 common contaminants found in LC-MS/MS experiments. More information can be found here.

--contamprefix

Mark the contaminant sequences with a prefix tag when downloading from Uniprot. This option only works when fetching a database from UniProt using the id flag

--custom

Skips the downloading of a fresh database and use an existing one instead. The custom file will also be used to create decoys and contaminants if desired.

--id

The Proteome ID used to find and download an organism proteome. See below where to find the ID.

--isoform

Allows isoform sequences to be added to the download.

--prefix

Decoy prefix to be added, default is rev_.

--reviewed

Download only reviewed sequences from Swiss-Prot.

--nodecoys

Do not add decoy (reversed) protein sequences.

Examples

Download a complete human proteome snapshot without isoforms, using Trypsin for protein digestion and adding contaminants.

philosopher database --id UP000005640 --contam

Download the reviewed version of the human proteome, containing isoforms and contaminants.

philosopher database --id UP000005640 --reviewed --contam

Prepare a custom protein FASTA file from an existing database, adding decoys and common contaminants.

philosopher database --custom protein.fas --contam

Download the complete human proteome and add external spike-in sequences from an existing FASTA file.

philosopher database --id UP000005640 --add spikes.fas

Download all reference sequences from the Human proteome, contaminants will be added, but no decoy sequences will be added.

philosopher database --contam --reviewed --id UP000005640 --nodecoys

FAQ

Where can I find the UniProt Proteome ID for my organism?

The list of all existing UniProt Identifiers can be found here. Before using Philosopher, you need to search the UniProt website for the correct id.