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
Tag
proteomics
Articles tagged proteomics. Tags group methods across clusters so a technique can be found from more than one route.
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
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16 articles
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
research sourcing
Commissioning a sequencing or proteomics study
Commission sequencing or proteomics by locking the question, the reference database, sample QC and the deliverable before a library or a digest is made.
8 October 2026 · 10 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
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
protein biochemistry
Detergents that ruin a later mass spec step
How SDS, Triton, NP-40 and Tween spoil a mass spectrum, which removal class to consider, and what to tell the person who will run it.
8 October 2026 · 9 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
Peptide fractionation overview
Single-shot runs versus offline peptide fractionation: depth, instrument time, sample use, concatenation and the losses that come with extra fractions.
8 October 2026 · 8 min read
proteomics
Post-translational modifications need extra evidence
Why a variable modification explains a mass shift without proving biology: localisation, neutral loss, search-space cost and which shifts are often tube artefacts.
8 October 2026 · 7 min read
proteomics
Preparing peptides for mass spectrometry
How laboratories prepare peptides for mass spectrometry: reduction, alkylation, digestion, cleanup, and the clues that a digest failed.
8 October 2026 · 7 min read
proteomics
Questions before a proteomics enquiry
Questions to write down before a proteomics enquiry: contrast, matrix, replicates, detergents, modifications, database, shipping temperature and the report fields you require.
8 October 2026 · 8 min read
proteomics
Reduction alkylation and trypsin
Why proteins are reduced and alkylated before trypsin in bottom-up proteomics, and how incomplete cysteine chemistry changes which peptides a search can name.
8 October 2026 · 11 min read