Proteomics, Metagenomics, and Bioinformatics Tools

A collection of vocabulary flashcards covering proteomics, protein interactions, metagenomics, and bioinformatics tools based on the lecture material.

Proteome

The complete set of proteins expressed by a cell, tissue or organism.

Proteomics

The large-scale study of proteins, including their structure, function and interactions.

Mass Spectrometry (MS)

An analytical technique that measures the mass-to-charge ratio ($m/z$) of ions.

MALDI

Matrix-Assisted Laser Desorption/Ionisation, a soft ionisation method used in mass spectrometry.

ESI

Electrospray Ionisation, a technique that ionises molecules from a liquid sample.

MS/MS (Tandem Mass Spectrometry)

Two rounds of mass spectrometry used to identify peptide sequences by fragmenting peptides to obtain sequence information.

Trypsin

An enzyme that digests proteins by cutting after lysine and arginine residues.

Peptide Mass Fingerprinting (PMF)

Identification of proteins by comparing peptide masses with theoretical peptide masses in databases.

Mascot

A search engine used to identify proteins from mass spectrometry data by matching it to protein sequence databases.

Protein-Protein Interaction (PPI)

A physical or functional interaction between two or more proteins.

Yeast Two-Hybrid (Y2H)

A method used to detect protein-protein interactions by activating a reporter gene in yeast.

BioGRID

A database of experimentally validated protein and genetic interactions.

STRING

A database of known and predicted protein interaction networks that integrates experimental evidence with computational predictions.

Interaction Network

A graphical representation of relationships between proteins.

Systems Biology

The study of biological systems by analysing interactions within complex systems and between their components.

Metagenomics

The study of genetic material recovered directly from environmental samples.

Microbiome

The community of microorganisms living in a particular environment.

16S rRNA Sequencing

A method used to identify and classify bacteria based on the conserved 16S ribosomal RNA gene.

Taxonomic Profiling

Identifying and determining which organisms are present in a microbial community.

Environmental DNA (eDNA)

DNA collected directly from environmental samples such as soil or water without isolating organisms.

Genome Browser

Software used to visualise genomes and gene annotations.

Annotation

The identification and description of genes or other functional elements within a genome.

Sequence Retrieval

Obtaining DNA, RNA or protein sequences from a database.

EMBOSS

A suite of open-source bioinformatics software tools.

Clustal Omega

Software used for multiple sequence alignment.

BLAST

A tool used to compare biological sequences against sequence databases to find similar nucleotide or protein sequences.

NCBI

A major bioinformatics resource containing genomic, protein and literature databases, mainly focusing on nucleotide data.

UniProt

A comprehensive protein sequence and annotation database specialising in protein functional annotations.

PDB

The Protein Data Bank containing three-dimensional structures of proteins and nucleic acids.

Ensembl

A genome browser providing annotated genomes for many species.

Proteome vs Genome

The proteome is the complete set of proteins, whereas the genome is the complete DNA sequence.

Metagenomics vs Genomics

Metagenomics studies DNA from mixed communities, while genomics studies the genome of a single organism.

MALDI vs ESI

MALDI uses a laser and matrix to ionise samples, whereas ESI produces ions from liquid samples using a high-voltage spray.