Omicser — Omics Engineer

Omics field

Proteomics

Proteomics is the large-scale study of the proteins produced by an organism, tissue or cell. It measures which proteins are detectable, in what amounts, and how they are modified — the layer closest to biological function.

Questions this field can answer

  • Which proteins are detectable in this sample, and at what relative abundance?
  • Which proteins change between conditions, and by how much?
  • Which post-translational modifications are present, and at which sites?
  • Which proteins interact or co-purify under defined conditions?
  • Does a transcript-level observation hold at the protein level?

Method

Research workflow

Established practice, from framing a question to depositing data others can reuse.

  1. 01

    Study design

    Define the comparison and the quantitative strategy up front — label-free, TMT or SILAC — and balance conditions across runs and labelling channels.

  2. 02

    Sampling

    Standardise lysis, protease and phosphatase inhibition, and storage. Protein degradation and modification start at collection.

  3. 03

    Assay and data generation

    Digest, optionally fractionate or enrich for a modification, then run LC-MS/MS in data-dependent or data-independent mode with a fixed gradient and instrument method.

  4. 04

    Quality control

    Track digestion efficiency, missed cleavages, retention-time stability, identification counts and QC pool reproducibility across the batch.

  5. 05

    Analysis

    Search spectra against a defined UniProt release with decoys, control peptide-spectrum-match and protein FDR at 1%, then normalize and model quantitative values.

  6. 06

    Interpretation

    Not detected does not mean absent. Shared peptides make protein inference ambiguous, and site localisation for PTMs needs its own confidence score.

  7. 07

    Reproducibility

    Report the exact database release, search engine, modifications, FDR method and normalization. Share the search parameter file.

  8. 08

    Deposition

    Deposit raw files, search results and metadata in PRIDE via ProteomeXchange, and cite the PXD accession.

Practice

Samples, technologies and what can go wrong

Method choice sets the ceiling on what an analysis can show. Limitations are part of the method, not an afterthought.

Sample types

  • Cell lysates and subcellular fractions
  • Tissue homogenates, fresh-frozen or FFPE
  • Plasma and serum, dominated by a few high-abundance proteins
  • Cerebrospinal fluid, urine and other biofluids
  • Immunoprecipitates and pull-downs for interaction studies
  • Secretomes from conditioned culture medium

Major technologies

Bottom-up LC-MS/MS
Proteins are digested to peptides before analysis; the standard approach, but protein-level identity must be inferred from peptides.
Top-down proteomics
Analyses intact proteoforms, preserving combinations of modifications, at lower throughput and higher difficulty.
Data-independent acquisition (DIA)
Fragments all precursors in fixed windows, giving more consistent quantification across runs and fewer missing values.
Isobaric labelling (TMT/iTRAQ)
Multiplexes samples in one run; efficient but subject to ratio compression.
Targeted assays (PRM/MRM)
High-precision measurement of a small pre-selected protein set, used for validation.

Limitations

  • Dynamic range: abundant proteins mask low-abundance ones, especially in plasma.
  • Non-detection is uninformative — it may be sensitivity, not absence.
  • Protein inference from shared peptides can be ambiguous.
  • PTM site localisation is often less certain than the modification call itself.
  • Missing values are frequent in label-free data and imputation changes results.

Common confounders

  • Batch and run-order effects, and instrument drift over long studies.
  • Sample handling time before freezing, which drives degradation.
  • Haemolysis and contamination in plasma and serum.
  • Incomplete or variable digestion between samples.
  • Unbalanced label channels across biological groups.

Live data

Search the public record

Read-only searches against public databases. Madomic presents and explains the records; the databases named below remain their source and owner.

Madomic Research Explorer

Search UniProtKB protein records

Live, read-only search of UniProtKB. Results come directly from UniProt and are capped at eight records per search; open each record to see the full curated entry.

Searches are capped and rate limited. Nothing you type is stored.

Reference

Glossary

Essential terms, in plain English.

PSM
Peptide-spectrum match — an assignment of one observed spectrum to one peptide sequence.
FDR
False discovery rate, usually estimated with a decoy database and controlled at 1%.
Protein inference
Deciding which proteins explain the identified peptides when peptides are shared.
PTM
Post-translational modification, such as phosphorylation, acetylation or glycosylation.
Label-free quantitation
Comparing intensities across separate runs without chemical labels.
TMT
Tandem mass tag: isobaric labels allowing several samples in one run.
DDA / DIA
Data-dependent versus data-independent acquisition strategies.
Proteoform
A specific molecular form of a protein, including its modifications and processing.
PXD accession
The public identifier of a dataset deposited in PRIDE through ProteomeXchange.

For students

Learning path and a practical activity

Everything below uses public data only. No samples, credentials or paid services are needed.

Learning path

  1. 01Learn how a mass spectrometer produces MS1 and MS2 spectra.
  2. 02Understand digestion, peptides and why bottom-up needs inference.
  3. 03Learn target–decoy FDR and why 1% is a convention, not a guarantee.
  4. 04Compare DDA and DIA, and the missing-value problem in each.
  5. 05Read a UniProt entry fully: evidence codes, features, isoforms, PTMs.
  6. 06Open a PRIDE dataset and read its experimental design file.
  7. 07Practise designing a PRM validation for three candidate proteins.

Activity — link a UniProt record to a public PRIDE dataset

  1. 01Search a protein of interest in the explorer below, for example “insulin” or “TP53”.
  2. 02Open a reviewed (Swiss-Prot) entry and record the accession, organism, sequence length and protein-existence evidence level.
  3. 03List two annotated post-translational modification sites and the evidence type behind each.
  4. 04In PRIDE Archive, search the same protein name or its gene, and open one dataset.
  5. 05Record the PXD accession, instrument, species and quantitation method, and note whether the design would detect your protein at all.
  6. 06Write three sentences comparing what UniProt asserts as curated knowledge with what that single experiment actually measured.

Attribution

Research resources

Authoritative public resources. Omicser is independent of each of them and links to the official source.

UniProt

Maintained by UniProt Consortium (EMBL-EBI, SIB, PIR)

Curated protein sequence and function knowledge, with evidence codes, features, isoforms and cross-references.

UniProt programmatic access

Maintained by UniProt Consortium

The official REST API guide for querying UniProtKB — the interface used by the explorer on this page.

PRIDE Archive

Maintained by EMBL-EBI

Public repository of mass-spectrometry proteomics data, including raw files, search results and experimental metadata.

PRIDE API guide

Maintained by EMBL-EBI

Documentation for programmatic search of public PRIDE projects and files.

Research and education use only. This page is not a clinical diagnosis, medical advice or a laboratory result. Verify every finding in the originating database and in the peer-reviewed literature before drawing conclusions.