Mass Spectrometry
MSAlso known as: mass spec
An analytical technique that measures the mass-to-charge ratio of ions to identify and quantify molecules in complex biological samples.
Mass Spectrometry (MS) is an analytical technique that ionizes molecules and separates the resulting ions by mass-to-charge ratio to identify and quantify analytes in biological samples 1.
How It Works
In a typical MS workflow, samples are ionized using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI). The ions are separated in a mass analyzer — common types include time-of-flight (TOF), quadrupole, ion trap, and Orbitrap — which measures their mass-to-charge ratios with high precision. Detectors record the abundance of ions at each m/z value, producing a mass spectrum.
Tandem mass spectrometry (MS/MS) fragments selected precursor ions and analyzes the resulting product ions, providing structural information for identification. Liquid chromatography (LC) is typically coupled upstream to separate complex mixtures before ionization, forming LC-MS/MS workflows essential for proteomics and metabolomics.
In synthetic biology, mass spectrometry quantifies intracellular metabolites, confirms protein identity and post-translational modifications, and measures pathway product titers with high specificity and sensitivity.
Computational Considerations
Peptide identification relies on database search engines such as MaxQuant, which match experimental MS/MS spectra against theoretical fragmentation patterns from protein sequence databases 2. Label-free quantification and isobaric labeling workflows extract relative or absolute protein abundances. Metabolomics data processing tools (XCMS, MZmine) perform peak detection, alignment, and annotation against spectral libraries. Statistical and machine learning methods then identify significant differences across experimental conditions.
Woolf Software builds computational pipelines for biological data analysis and experimental design optimization. Get in touch.
Database search engines and de novo sequencing algorithms match experimental spectra to peptide or metabolite identities, while quantification software extracts ion intensities across samples.