Serum Proteomics Analysis
Cross-cohort analysis of the Chinese serum proteomics datasets indexed in the Human Immune Atlas — the Han Chinese serum proteome pQTL (GNHS + WEBIRTH, 2,958 cohort) panel and its coverage in the CIMA immune atlas, the shared core proteome across three cohorts, and the RA serum differential analysis.
Dataset Status
| Dataset | Cohort | Assay | Protein / Genes | Per-sample matrix | Repository |
|---|---|---|---|---|---|
| GNHS + WEBIRTH (WeBirth) | 2,958 Han Chinese (GNHS), GWAS meta 2,410 | Serum DIA-MS (TripleTOF 5600), DIA-NN compatible | 304 / 300 | No matrix (wiff no MS2) Not public (wiff raw lacks MS2; DIA-NN cannot extract) | iProX PXD039231 (GNHS), PXD038253 (WEBIRTH) Nature Communications 2023, doi:10.1038/s41467-023-36491-3 |
| CRC plasma proteomics, Zhejiang (ZJU 2nd) | 250 (150 CRC + 50 control + 50 AA) | TMT-6plex plasma proteomics | 31,673 / 2,287 | Official matrix Official MaxQuant matrix available (TMT, 250 samples) | iProX PXD054569 |
| RA serum proteomics, Guangzhou | 8 HC + 28 RA (36 samples) | Serum LC-MS/MS LFQ | 10,680 / 1,052 | Official matrix Official MaxQuant LFQ matrix available (109 columns) | PRIDE PXD032912 |
The pQTL (GNHS + WEBIRTH) raw WIFF files contain no MS2 spectra and the per-sample protein abundance matrix was never published, so sample-level quantification cannot be re-derived; only the curated 304-protein panel and its published pQTL / genetic-association results are available. CRC (TMT) and RA (LFQ) datasets ship official MaxQuant per-sample matrices.
GNHS 304-Protein Panel × CIMA Immune Atlas Coverage
Panel detection & top expressed proteins
Triple-cohort shared core proteome
Top-30 GNHS panel proteins by expressing cells (CIMA immune atlas)
| # | Gene | Expressing cells | % of 6.48M |
|---|---|---|---|
| 1 | ITGAL | 4,140,543 | 63.85% |
| 2 | IGKC | 3,552,863 | 54.79% |
| 3 | SELL | 3,442,821 | 53.09% |
| 4 | PEBP1 | 3,211,200 | 49.52% |
| 5 | IGHM | 2,637,213 | 40.67% |
| 6 | SEMA4D | 2,218,056 | 34.20% |
| 7 | INPP5D | 2,186,754 | 33.72% |
| 8 | IGHA1 | 2,062,753 | 31.81% |
| 9 | FLOT2 | 1,946,486 | 30.02% |
| 10 | HBB | 1,608,129 | 24.80% |
| 11 | EHBP1L1 | 1,571,733 | 24.24% |
| 12 | EIF3B | 1,449,483 | 22.35% |
| 13 | MBTPS1 | 1,428,290 | 22.02% |
| 14 | WHAMM | 1,413,975 | 21.80% |
| 15 | PPP2R1A | 1,398,153 | 21.56% |
| 16 | DOCK11 | 1,385,774 | 21.37% |
| 17 | MRPS34 | 1,339,005 | 20.65% |
| 18 | LPIN1 | 1,301,464 | 20.07% |
| 19 | PF4 | 1,298,648 | 20.03% |
| 20 | KIAA2026 | 1,210,209 | 18.66% |
| 21 | UHRF2 | 1,208,725 | 18.64% |
| 22 | PPBP | 1,165,644 | 17.97% |
| 23 | HIPK1 | 1,093,053 | 16.86% |
| 24 | FRYL | 1,068,657 | 16.48% |
| 25 | SIRT7 | 1,040,578 | 16.05% |
| 26 | USP20 | 960,433 | 14.81% |
| 27 | RFC1 | 939,479 | 14.49% |
| 28 | MTA1 | 929,606 | 14.33% |
| 29 | DPM3 | 929,307 | 14.33% |
| 30 | PSME4 | 924,853 | 14.26% |
Panel genes not mapped in the immune atlas
ATP5L2 · FAIM3 · GCN1L1 · ICT1 · IGJ · MUC16 CA125 · NA · SEPP1 · SGK223 · ST13P5 FAM10A5 · YAE1D1
Shared Core Proteome (138 genes)
| GNHS ∩ CRC | (of GNHS) | GNHS ∩ RA | (of GNHS) | CRC ∩ RA | Three-way |
|---|---|---|---|---|---|
| 149 | 49.7% | 146 | 48.7% | 819 | 138 |
Three-way core set (138 genes) is dominated by complement, apolipoprotein / lipid transport, coagulation / serpin, immunoglobulin, and acute-phase plasma proteins — the conserved circulating proteome shared across independent Chinese serum panels.
RA Serum Differential (23 proteins, FDR<0.05)
RA vs HC volcano — 14 up / 9 down (FDR<0.05)
Significant proteins (by |log2FC|)
| Gene | log2FC (RA vs HC) | FDR | Mean HC | Mean RA | Direction |
|---|---|---|---|---|---|
| APCS;HEL-S-92n | +3.533 | 7.20e-06 | -4.14 | -0.61 | up |
| SAA2 | +2.175 | 2.69e-02 | -1.01 | 1.17 | up |
| ALB | -1.446 | 2.69e-02 | 1.22 | -0.22 | down |
| IGHG4 | -1.299 | 7.91e-03 | 1.14 | -0.15 | down |
| HSP90B1;TRA1;HEL-S-125m | +1.298 | 1.77e-02 | -1.34 | -0.04 | up |
| APOC4 | -1.287 | 1.77e-02 | 1.13 | -0.16 | down |
| APMAP | +1.231 | 3.04e-02 | -0.87 | 0.36 | up |
| GP5 | -1.166 | 2.53e-02 | 0.56 | -0.61 | down |
| DKFZp686P15220 | +1.149 | 7.91e-03 | -0.93 | 0.22 | up |
| PCOLCE | +1.144 | 3.17e-02 | -1.01 | 0.14 | up |
| +0.900 | 3.42e-02 | -0.71 | 0.19 | up | |
| HYOU1 | +0.852 | 1.77e-02 | -0.56 | 0.29 | up |
| HMFT1766 | +0.810 | 2.95e-03 | -0.66 | 0.15 | up |
| F5 | +0.782 | 4.51e-02 | -0.75 | 0.03 | up |
| DPEP2 | +0.761 | 3.74e-02 | -0.71 | 0.06 | up |
| +0.714 | 3.74e-02 | -0.68 | 0.04 | up | |
| C1QB | -0.666 | 2.76e-04 | 0.54 | -0.13 | down |
| PRG4 | +0.662 | 3.74e-02 | -0.37 | 0.29 | up |
| ITIH2 | -0.606 | 3.74e-02 | 0.48 | -0.13 | down |
| CDH13 | -0.587 | 2.06e-02 | 0.41 | -0.17 | down |
| CD14 | +0.468 | 2.95e-03 | -0.34 | 0.13 | up |
| AFM | -0.464 | 1.87e-02 | 0.34 | -0.12 | down |
| AHSG | -0.413 | 2.62e-02 | 0.37 | -0.05 | down |
RA differential from PXD032912 (8 HC, 28 RA, LFQ). Top hits APCS (+3.53), SAA2 (+2.17) and SAA1, CD14 elevation, and ALB / IGHG4 reduction are consistent with the published acute-phase / autoantibody signatures.
Source analysis: pandora002 /mnt/disk1/ChineseImmuneAtlas20260707/proteomics/iprox_meta — cross_analysis_result.json
(2026-08-09) & PXD032912 differential (2026-08-09). Generated 2026-08-11.