proteomics
Label-free versus labelled quantification
When a label-free fold change disagrees with a blot, or a labelled ratio looks compressed, check missing values, batch effects, shared peptides and
8 October 2026 · 9 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
Missed cleavages and ragged ends
How an internal lysine or arginine differs from a ragged peptide end, what a high missed-cleavage rate says about the digest, and how search settings affect the
8 October 2026 · 10 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
Phosphoproteomics sample handling
Phosphates disappear to phosphatases at lysis and during warm, alkaline waits. Handling, enrichment class and site-localisation evidence decide whether a
8 October 2026 · 9 min read
proteomics
Plasma and the dynamic range problem
Plasma and serum span many orders of magnitude in protein concentration. A plain digest mostly sees albumin and immunoglobulins, and depletion changes what
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
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
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
proteomics
Sample randomisation and batch design
How sample randomisation and blocking stop a processing day from masquerading as biology, and why a confounded proteomics batch often cannot be rescued later.
8 October 2026 · 7 min read
proteomics
Targeted MRM versus discovery runs
When to screen with a discovery run and when to confirm with targeted MRM: peptide choice, transitions, a matrix blank and a calibration or labelled standard.
8 October 2026 · 8 min read
proteomics
TMT and iTRAQ as concepts
TMT and iTRAQ are isobaric reagent classes: one precursor mass, reporter ions for quantity, and ratio compression when other peptides are co-isolated.
8 October 2026 · 8 min read