Proteomics (mass-spec CRO)

01Overview and value chain

Markers: [EC: CLIA / CAP (US) + ISO 17025 + GDPR (EU) | OECD: Genomics & bioinformatics | Regulator: FDA (USA), EMA (EU), NMPA (China)]

Proteomics as a service outsources large-scale protein identification and quantification to specialized contract research organizations (CROs), using LC-MS/MS and affinity assays to drive biomarker discovery, pharmacoproteomics and drug-target deconvolution. Data-Independent Acquisition (DIA) now profiles thousands of proteins per sample with high reproducibility and no missing values, making deep proteome maps a routine B2B deliverable. The stack runs from sample preparation (SP3, iST, S-Trap digestion) through nano-LC separation (Evosep One) and high-resolution mass spectrometry (Orbitrap Astral, timsTOF) to bioinformatics (DIA-NN, Spectronaut, MaxQuant against UniProt) and statistically validated reporting. Clinical-grade labs operate under CLIA/CAP accreditation (US), ISO 17025, and EU GDPR for patient data. The six organizations in this projection span DIA software and service (Biognosys), CRO capacity (Evotec, WuXi AppTec), affinity proteomics (Olink, Somalogic) and sample preparation (ProtiFi).

Key directions of proteomics as a service:

1. DIA deep proteome profiling: thousands of proteins per sample with high reproducibility and no missing values (Spectronaut, DIA-NN).
2. Affinity proteomics at scale: PEA (Olink) and aptamer (SomaScan) platforms for high-plex plasma profiling without mass spectrometry.
3. Pharmacoproteomics and target deconvolution: LiP-MS and host-cell- protein analysis for drug mechanism-of-action studies.
4. High-throughput sample preparation: S-Trap and Evosep One standardization to drive down run-to-run variability.

Sectoral value chain

[sample prep] ──> [desalting] ──> [LC separation] ──> [MS acquisition]
                                                          │
                                                (bioinformatics)
                                                          │
                                                          ▼
[B2B report] <─── [statistics] <─────┘

Value chain levels

Cross-cutting technologies of the sector:

• mass-spectrometry: high-resolution LC-MS/MS (Orbitrap Astral, timsTOF) with DIA acquisition.
• dia-proteomics: library-free DIA with neural-net deconvolution (DIA-NN, Spectronaut).
• affinity-proteomics: PEA and aptamer platforms for high-plex plasma proteomics.

02US

The United States leads affinity-proteomics platforms and clinical-accredited CRO services tightly integrated into drug-development pipelines.

affinity platforms, clinical accreditation, sample prep

• Somalogic (Standard BioTools): the SomaScan aptamer platform; its SomaScan Select 4K assay quantifies around 4,000 proteins from a small plasma sample.
• Olink Proteomics (Thermo Fisher): Proximity Extension Assay (PEA) panels read out by qPCR/NGS on the Olink Signature Q100 instrument for high-specificity plasma proteomics.
• ProtiFi: the S-Trap sample-preparation technology (including 96-well micro plates) that standardizes digestion and lowers run-to-run variability.
• CLIA/CAP accreditation: US labs delivering diagnostic proteomics must meet Clinical Laboratory Improvement Amendments and College of American Pathologists standards.

03CN

China treats proteomics as a strategic national discipline and runs the world’s largest capacity build-out for deep proteome mapping.

national centers, cost-competitive CROs, instrument localization

• CNPHen (National Center for Precision Medicine, Beijing/Shanghai): large proteome centers running dozens of latest-generation Orbitrap Astral and timsTOF Ultra instruments around the clock.
• WuXi AppTec (SSE 603259) and BGI Proteomics: offer deep plasma and tissue proteome profiling for biomarker and preclinical studies, making China a cost-competitive global outsourcing hub.
• Instrument localization: domestic nano-LC systems and custom column sorbents to reduce dependence on imported consumables.

04EU

The European Union leads DIA software, premium pharmacoproteomics CROs and the international standards bodies, under strict GDPR data governance.

DIA software leadership, pharmacoproteomics, GDPR

• Biognosys (Schlieren, Switzerland; Bruker): the Spectronaut DIA analysis software (the field’s gold standard; Spectronaut 21 and SpectroMine 6 showcased at ASMS 2026), plus TrueDiscovery deep-proteome services on timsTOF.
• Evotec (Germany): high-throughput proteomics on the Orbitrap Astral, including quantitative host-cell-protein analysis of antibody therapeutics and target identification.
• HUPO standards and GDPR: the Human Proteome Organization sets international validation rules, while EU CROs operate multi-omics platforms (spatial transcriptomics plus spatial proteomics) under strict patient-data governance.

05Leading companies and research institutes

06Tech stack and innovations

The stack combines chromatography, high-resolution mass spectrometry and neural-network bioinformatics, complemented by affinity proteomics.

1. Nano-LC and high-resolution MS:
   • Evosep One nano-LC separates peptides on C18 columns, feeding the Orbitrap Astral (high-speed acquisition) or Bruker timsTOF (trapped ion-mobility separations) operating in DIA or DDA mode.
2. DIA acquisition and bioinformatics:
   • library-free DIA is deconvolved by neural-network software (DIA-NN) and Biognosys’ Spectronaut, with MaxQuant for DDA label-free quantification against UniProt, controlled to a peptide and protein FDR below 1%.
3. Affinity proteomics:
   • Olink’s PEA (dual-antibody recognition with PCR/NGS readout) and Somalogic’s SomaScan (slow off-rate aptamers) quantify thousands of plasma proteins without mass spectrometry, broadening access to high-plex proteomics.

07Value chains and production pipelines

Industrial pipeline of a clinical plasma proteome profile (ISO 17025)

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Sample preparation     │ ───> │ 2. Digestion              │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. LC-MS/MS acquisition   │ <─── │ 3. Desalting              │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Bioinformatics         │ ───> │ 6. Statistics & report    │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Sample preparation

Plasma or tissue samples are received and checked for haemolysis, then lysed in a denaturing buffer to solubilize the full protein content.

Stage 2: Digestion

Disulfide bonds are reduced and alkylated, and sequencing-grade trypsin digests proteins into peptides of optimal length and charge for mass spectrometry.

Stage 3: Desalting

Peptides are cleaned on C18 StageTips to remove salts and buffers that would otherwise suppress ionization, then dried and reconstituted in loading solvent.

Stage 4: LC-MS/MS acquisition

Peptides are separated by nano-LC and measured in DIA mode on a high-resolution Orbitrap or timsTOF instrument, with periodic QC injections to monitor retention-time and signal stability.

Stage 5: Bioinformatics

Raw spectra are processed in DIA-NN or Spectronaut against the UniProt FASTA database, identifying and quantifying proteins at a false-discovery rate below 1%.

Stage 6: Statistics and reporting

Differential expression is computed (volcano plots, ANOVA), enriched pathways are mapped (KEGG, Reactome), and a validated B2B report is delivered to the client’s LIMS portal.