proteomics
A glossary of proteomics terms
A working glossary of proteomics terms, from precursor and PSM to razor peptide, FDR and batch effect, and how each term changes a pull-down or abundance claim.
8 October 2026 · 8 min read
Topic cluster
Proteomics
Bottom-up mass spectrometry, peptide preparation, identification and what a proteomics report does and does not prove.
All topicsBuffers and laboratory water26Cell culture26Chromatography26Cold chain and sample storage26Cytometry and microscopy26DNA sequencing26Gels and blotting26Gene expression26Genome editing26Immunoassays26Laboratory labware26Laboratory safety26Liquid handling26Microbiology26Molecular cloning26Nucleic acid purification26PCR and amplification26Protein biochemistry26Proteomics26Research sourcing and study design26
proteomicsenquiryglossarytroubleshootingcontaminationquantificationstudy designpeptidesblanksevidencemass spectrometryreportingcarryoverdetergentsauditbatch effectschromatographydda
26 articles
proteomics
A protein ID is not a proof of function
A proteomics identification is a sequence match under a false discovery rate. Function still needs activity, phenotype, localisation or a perturbation, plus controls.
8 October 2026 · 8 min read
Pillar · proteomics
Bottom-up proteomics in plain language
Bottom-up proteomics in plain language: proteins are digested to peptides, a mass spectrometer fragments them, and a database search names candidates.
8 October 2026 · 7 min read
proteomics
Chromatography before the mass spectrometer
Reversed-phase C18 is the usual peptide separation before electrospray. Trap-elute or direct injection, and nano versus higher flow, are column specification choices.
8 October 2026 · 8 min read
proteomics
Comparing DIA and DDA for a first study
Choosing DIA or DDA for a first study of twelve samples and two conditions, including missing values, a predicted library and what a power cut does to the queue.
8 October 2026 · 7 min read
proteomics
Data-dependent and data-independent acquisition
How data-dependent acquisition picks tall precursors and data-independent windows fragment a mass range, and which choice fits discovery or a repeated panel.
8 October 2026 · 8 min read
proteomics
Database choice changes the identifications
How taxon, reviewed versus unreviewed sequences, contaminants and a custom fusion entry change proteomics identifications, and why the decoy must match.
8 October 2026 · 8 min read
proteomics
Detergents salts and why they matter
Why SDS, other detergents and leftover salts suppress electrospray, which cleanup classes remove them, and how a flat ion current with a normal UV trace should be read.
8 October 2026 · 10 min read
proteomics
False discovery rates and decoy searches
A decoy search estimates the false discovery rate of a whole accepted list. It is not the probability that one protein is true, and it does not repair a wrong database.
8 October 2026 · 8 min read
proteomics
From spectra to a biological claim
From a raw spectrum to a sentence a biologist may say: identification, a designed contrast, an orthogonal check, and the claim a cell study can actually support.
8 October 2026 · 7 min read
proteomics
Injection amounts and column loading
Too little peptide yields sparse identifications. Too much broadens peaks, saturates the detector and carries into the next blank. Load follows the column, not a universal volume.
8 October 2026 · 8 min read
proteomics
Keratin contamination from the bench
Skin, hair, wool and dust shed keratins that can dominate a weak proteomics sample. A blank and the keratin types separate bench contamination from tissue.
8 October 2026 · 9 min read