Boster's discovery proteomics service measures thousands of proteins across your samples by LC-MS/MS without a predefined target list. Use it when you need to know which proteins change between conditions and don't yet have a candidate list.
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is the standard method for proteome-wide discovery work. Antibody-based multiplex panels also quantify many proteins, but only ones chosen beforehand. Work is delivered through Boster and its partner labs.
What the Discovery Proteomics Service Includes
Each project covers the steps from sample to report. Scope is set with you at the quote stage.
Sample Preparation and Digestion
Protein extraction, reduction and alkylation, and enzymatic digestion of proteins into peptides, typically with trypsin.
LC-MS/MS Acquisition
Peptides are separated by liquid chromatography and analyzed by tandem mass spectrometry in data-dependent (DDA) or data-independent (DIA) mode.
Quantitation
Label-free or TMT-multiplexed quantitation to compare protein abundance across treatment groups, time points or research cohorts.
Protein Identification
Proteins in gel bands, spots or purified samples are identified by LC-MS/MS peptide analysis and database searching.
Bioinformatics Report
Protein identification and quantification tables, differential-abundance statistics, pathway enrichment and QC metrics.
Study Scoping
Comparison groups, replicates, acquisition mode and quantitation method are agreed before samples ship.
A phosphoproteomics service is available on request to profile phosphorylation sites and compare their relative abundance between conditions.
Discovery First, Then Validation
Discovery proteomics profiles proteins without a predefined target list. Proteins are digested into peptides, the peptides are separated and fragmented, and the data are searched to identify and quantify as many proteins as the sample allows, often several thousand per run with DIA. It is the right starting point when you need a candidate list or want to compare whole proteomes between conditions.
Targeted assays measure selected proteins and can offer greater sensitivity for those targets, supporting follow-up across many samples. Once discovery gives you a shortlist, hits can be checked with multiplex assay services, or one protein at a time with a western blotting service or IHC and histology services.
Discovery proteomics compared with targeted follow-up assays
Criterion
Discovery proteomics
Targeted follow-up
Coverage
Broad profiling without a predefined target list
A defined panel of candidates
Sensitivity
Moderate; low-abundance proteins may be missed
Can be higher for selected targets
Typical study size
Pilot or discovery cohort
Larger validation cohorts
Best use
Hypothesis generation, candidate screening
Confirming and quantifying hits
Rule of thumb: if you can't yet list the proteins you expect to change, start with discovery.
Quantification & Acquisition Options
Label-free and TMT are quantification strategies; DDA and DIA describe how MS/MS data are acquired.
The quantitation method depends on sample number, the depth you need and how much run-to-run consistency matters.
Label-Free Quantification
Peptide intensities are compared across separately run samples. There is no labeling step and it scales to large sample numbers, but it is more sensitive to run-to-run variation, so consistent sample prep and randomized run order matter.
TMT Multiplexing
Peptides from each sample are tagged with isobaric labels and pooled for analysis. This supports consistent comparisons within a batch; batch size depends on the TMT format.
Data-Independent Acquisition (DIA)
DIA systematically fragments precursor ions within defined mass-to-charge windows. Combined with label-free quantification, it supports broad, reproducible protein profiling.
Method
Throughput
Reproducibility
Depth
Best fit
Label-free (DDA)
High; samples analyzed individually
Moderate
Good
Large sample sets, budget-sensitive studies
TMT
Moderate (batch-limited)
High
Very good
Precise multi-condition comparisons
Label-free DIA
High
Very high
Very good
Large cohorts needing depth and consistency
A large research cohort usually favors label-free DIA for throughput. TMT can suit multi-condition studies that fit within a multiplexed batch.
Workflow: From Sample to Report
Project Scoping
The research question, comparison groups, replicate structure, acquisition mode and quantitation method are agreed first. Timeline and price are quoted per project.
Sample Submission
You ship samples that meet the agreed input and preservation requirements, with a completed sample manifest.
Sample Preparation
Proteins are extracted, reduced, alkylated and digested into peptides. Fractionation is available on request.
LC-MS/MS Acquisition
Peptides are separated by liquid chromatography and analyzed by tandem mass spectrometry in DDA or DIA mode.
Data Analysis and Report
Raw spectra are processed into identified and quantified proteins, followed by statistical comparison, QC review and pathway analysis.
Sample Types and Preparation
Good sample collection and preservation are essential for reliable proteomics results.
Common Sample Types
Cultured cells and cell pellets
Fresh-frozen tissue
Plasma and serum
Purified proteins and gel bands
Immunoprecipitates and pull-down eluates
Other sample types can be discussed at quote.
Preservation and Shipping
Snap-freeze tissue and cell samples and ship on dry ice
Avoid repeated freeze-thaw cycles, which degrade proteins and can introduce artifactual modifications
Use protease inhibitors compatible with the agreed preparation workflow.
Minimum protein input is confirmed at quote, before you collect
Fractionation Options
For complex samples, peptide fractionation before LC-MS/MS adds depth at the cost of extra preparation and instrument time. It is available on request:
Method
Purpose
Typical use
Strong cation exchange (SCX)
Separates peptides by charge before MS analysis
Deep profiling of complex lysates
High-pH reverse phase
Separation orthogonal to on-line low-pH reverse phase, reducing co-elution
TMT studies needing extra depth
Bioinformatics and Deliverables
The analysis turns raw spectra into results you can act on: which proteins changed, by how much, with what confidence, and which pathways they point to.
Deliverables are quoted per project and can include a written summary, protein and peptide identification and quantification tables, differential-abundance results, pathway enrichment output and QC metrics. Raw and processed files can be included in the deliverables.
Statistical Analysis
Differential-abundance testing between conditions with multiple-testing correction, reporting effect sizes and confidence rather than raw p-values alone.
Pathway and Network Interpretation
Gene Ontology and pathway enrichment, and protein-protein interaction network mapping, to place changed proteins in biological context.
Quality-Control Metrics
Chromatographic performance, identification false discovery rates (FDR), missed-cleavage rates and sample-level QC metrics help assess dataset quality.
Research Applications
Proteins, not transcripts, are usually the direct targets, mediators or biomarkers in a study, which makes discovery proteomics useful at several points in a research program.
Target Identification
Compare disease and control models, or treated and untreated samples, to identify proteins associated with a phenotype.
Biomarker Discovery
Screen research cohorts, including human plasma or tissue samples, for candidate biomarkers, then confirm the hits with targeted assays.
Mechanism of Action
Profile protein-abundance changes after treatment to identify pathways associated with the response.
Planning a Discovery Study?
When choosing a proteomics CRO, discuss sample requirements, acquisition options and deliverables before collection. Boster’s protein analysis services can be tailored to your research question. For follow-up work, see Boster’s assay services.
GLP and other quality requirements are confirmed for each project before quotation.
Frequently Asked Questions
How much sample do I need?
Minimum protein input depends on sample type and study design and is confirmed at quote. Settling it before collection avoids the most common cause of project delay.
How long does a project take, and what does it cost?
Timeline and price depend on sample number, acquisition mode and whether fractionation is needed. Both are quoted per project.
How are discovery hits validated?
A discovery run produces a candidate list. Candidates are then confirmed in a larger sample set with targeted methods such as multiplex immunoassays, western blot or IHC.
Do you provide raw data, or only a summary report?
Raw and processed files can be included in the deliverables alongside the written report.
Does discovery proteomics measure absolute protein concentrations?
Standard label-free and TMT workflows measure relative protein abundance. Absolute quantification requires a dedicated assay and suitable standards.
How many proteins will be identified in my samples?
Coverage depends on sample type, preparation, instrument and acquisition method. Expected depth is discussed during project planning.
