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.

--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 for the analysis (skip the download).

philosopher database --custom protein.fas --contam

Download the complete human proteome and add external sequences from another FASTA file.

philosopher database --id UP000005640 -add spikes.fas

This example will download all reference sequences from the Human proteome, contaminants will be added to the database with the rev_ prefix and the resulting file will be digested using Lys C.

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

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.