MaCPepDB - Mass Centric Peptide Database

MaCPepDB creates and maintains a peptide database and provides a web API for accessing the database.

Note: This is the next iteration of MaCPepDB, moving from the previous Python-implementation to Rust and using ScyllaDB instead of PostgreSQL / Citus, in order to get better performance and make MaCPepDB ready to include more data.

Ambiguous amino acids

Some UniProt entries contain one letter codes which encode multiple amino acids. Usually the encoded amino acids have a similar or equal mass. Ambiguous one letter codes are:

• B encodes D & N
• J encodes I & L
• Z encodes E & Q

Because the amino acids encoded by B & Z have a different mass and only a few hundreds entries contain these, MaCPepDB resolves the ambiguity by creating all possible combination of the peptide with the distinct amino acids, e.g.:

ambiguous peptide	distinct peptides
PE_B_TIDE_Z_K	PE_D_TIDE_E_K
	PE_D_TIDE_Q_K
	PE_N_TIDE_E_K
	PE_N_TIDE_Q_K

J encodes Leucine and Isoleucine, both have the same mass. Resolving those would not make the peptides better distinguishable by mass.

In theory X is also ambiguous, encoding all amino acids. Practically a lot more entries containing X than the previous mentioned ambiguous amino acids, sometimes with a high abundance of X. Resolving these would increase the amount of peptides significantly and slowing down MaCPepDB's search functionality.

Input

• Protein data are provided by UniProt Text/EMBL format (
  • Documentation
  • Source (dat-files) or on UniProt download as Text
• Taxonomy data are provided
  • Documentation
  • Source (taxdump.zip)

Database structure

MaCPepDB utilizes a denormalized database structure for efficient record storage and compatibility with various database engines. Denormalization consolidates data into fewer tables, minimizing redundant data such as multi-column primary key of peptides. However, this approach may result in a loss of certain SQL functionalities, such as foreign keys and cascade operations that ensure database integrity. To compensate for this, the lost functionality is implemented in the application code. Manual alterations to the database are discouraged and should be done using MaCPepDB.

Configuration

Table: config

Column	Type	Data
conf_key	String (max. length 256)	key to find configuration value
value	JSON	Value of configuration key wrapped in a JSON object: {"wrapper": value>}

Proteins

Table: proteins

Column	Type	Data
accession	text	Primary accession in UniProt
secondary_accessions	list	Secondary or old accessions after merges
entry_name	text	Entry name in UniProt
name	text	Human readable name
genes	list	Containing genes
taxonomy_id	bigint	Taxonomy ID
proteome_id	text	Proteome ID
is_reviewed	boolean	true if SwissProt otherwise false
sequence	text	Amino acid sequence
updated_at	bigint	Last entry update in UniProt (Unix timestamp)
domains	frozen<set>	Set of domains associated with the protein

* primary key is bold

Peptides

Column	Type	Data
partition	bigint	A partition key based on the mass to cluster peptides
mass	bigint	Theoretical mass as integer
sequence	text	Amino acid sequence
missed_cleavages	smallint	Number of missed cleavages
aa_counts	list	Containing the amino acid counts
proteins	set	Primary accession of containing proteins
is_swiss_prot	boolean	true if contained by a protein in SwissProt
is_trembl	boolean	true if contained by a protein in TrEMBL
taxonomy_ids	set	IDs of containing taxonomies
unique_taxonomy_ids	set	IDs of taxonomies with only one protein containing this peptide
proteome_ids	set	IDs of containing proteomes
domains	frozen<set>	Set of domains in which the peptide occured
is_metadata_updated	Boolean	true if metadata is up to date (internal use only)

* primary key is bold

Domain

This is a ScyllaDB user defined datatype.

Column	Type	Data
name	text	Name
evidence	text	Evidence reference
start_index	bigint	Start offset at which the domain begins (relative to the overall protein/peptide sequence)
end_index	bigint	End index (^)
protein	text	The protein accession of the protein that contains the peptide and domain that is within the peptide range (this column empty for the Protein table)
start_index_protein	bigint	Start index of domain for the protein sequence (this column empty for the Protein table)
end_index_protein	bigint	End index of domain for the protein sequence (this column empty for the Protein table)
peptide_offset	bigint	Start index of the peptide sequence within the protein

Blobs

Table to store several binary data. Scylla blob type has in practice a limit of < 1MB, therefore data is stored in multiple chunks of max 512KB. Each chunk has a prefix and chunk index as key.

Column	Type	Data
key	string	prefix_<CHUNK_NUMBER>
data	blob	Chunk of binary data with max. 512 KB

* primary key is bold

Scylla Cluster Deployment

Install Scylla

Ubuntu 22.04

Configure

For every node in the cluster:

Edit /etc/scylla/scylla.yaml and

• set the seed to the IP of the first node in the cluster
• Set listen-address and rpm-address to the IP of the current node
• Set the same cluster name
• Use GossipingPropertyFileSnitch as a snitch

Edit /etc/scylla/cassandra-rackdc.properties and

• uncomment and name dc and rack

Scylla Setup

For every node in the cluster:

• Run scylla_setup and use XFS setup on the desired drive
• Don’t use io tuner during setup
• Enable dev mode: sudo scylla_dev_mode_setup —developer_mode 1
• sudo systemctl start scylla-server

You can try using io tuner for your disk, however in some cases the performance with io tuner and non-devmode seems worse than performance with no iotuner and devmode enabled

Usage

Build

To build the database use cargo run -r -- build .... Use --help for all options.

Database URL

Connection settings to database given via an URL: scylla://[user:password@]<comma_separated_list_of_hosts>/<keyspace>[?attirbute1=foo&attribute2=bar&...]

Supported attributes (see: https://docs.rs/scylla/latest/scylla/transport/session_builder/type.SessionBuilder.html)

Attribute	Type	Description
connection_timeout	usize	In seconds
pool_size	usize
pool_type	String	Per host or per shard, only applied when pool_size is given (possible values: host, shard, default: host)

Recommendations

1. Use MaCPepDB's sub commands mass-count and partitioning to generate balanced peptide partitions before building the database. Once the masses are counted you can use the resulting file to generate different peptide partitions you can use with the build command to find an optimum. E.g. for complete Uniprot a couple million peptides per partitions were the optimum. Depending on your hardware and protein collection it will change.

Impact of protease

Most metrics you encounter are obtained using Trypsin for digestion. Be aware that a different protease will generate other metrics. E.g. digesting the Mus Musculus proteome using Trypsin and Unspecific produce (obviously) very different results. Better hardware and much more disc space is required for an unspecific digest as on can imagine.

protease	peptides	distinct masses
trypsin	421062	359760
unspecific	84759305	37876354

Web API

cargo run -r web scylla://<COMMA_SEPARATED_SCYLLA_NODES_LIST>/<KEYSPACE/DATABASE> <IP> <PORT>

Citation

MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKB
Julian Uszkoreit, Dirk Winkelhardt, Katalin Barkovits, Maximilian Wulf, Sascha Roocke, Katrin Marcus, and Martin Eisenacher
Journal of Proteome Research 2021 20 (4), 2145-2150
DOI: 10.1021/acs.jproteome.0c00967

Posters about further development

• MaCPepDB: Increasing the performance of the mass centric peptide database with old hardware and a distributed database
• Enhancements of MaCPepDB – the Mass Centric Peptide Database