What it is
Canonical name: Proteomics. 1
Known aliases: No additional aliases are reported in this document. 1
Stable external identifier: Not applicable or reported for this method in the document. 1
Proteomics measures protein expression and was used as an independent evidence axis alongside flux-balance-analysis, tnseq, complete-gene knockout phenotypes, and mutant growth measurements in the study of acinetobacter-baylyi-adp1. 1
Evidence from adp1_triple_essentiality
Proteomics measured average log2 expression across 7 Acinetobacter strains for 2,288 genes. 1
Among these genes, essential genes (n = 464) had mean log2 expression of 28.43 ± 2.94, whereas dispensable genes (n = 1,824) had mean log2 expression of 25.73 ± 2.96. 1
Essential genes therefore showed a difference of 2.70 log2 expression units, corresponding to 6.5-fold higher expression than dispensable genes. 1
The difference in expression between essential and dispensable genes was statistically significant by the Mann–Whitney U test, with p = 9.91×10⁻⁵⁹. 1
Expression correlated with knockout essentiality at Pearson r = 0.345 (p = 5.32×10⁻⁶⁵) and Spearman ρ = 0.338 (p = 3.28×10⁻⁶²). 1
Proteomic expression classified knockout essentiality with ROC AUC = 0.743, where AUC means Area Under the ROC Curve, a threshold-independent classification measure. 1
These results support multi-omics-integration by showing that proteomics provides a complementary continuous predictor alongside flux-balance analysis (FBA), fitness, knockout, and TnSeq evidence. 1
Evidence from caulobacter_fur_lipida_loss
Single-replicate outer-membrane proteomics in caulobacter-crescentus refines the existing complementary-evidence claim: it was used with transcriptomics, RB-TnSeq fitness, published regulons, and comparative annotation to examine envelope remodeling rather than to quantify essentiality directly. 2
The protein measurements support transcript–protein discordance in the Lpt apparatus: LptD changed by log2(4672/4659) = -0.47 and by log2(4672/4580) = -0.62, while LptE changed by -0.78 and -0.68, despite transcript-level increases for MsbA-like CCNA_00307 (+0.89, FDR 0.01) and LptC-related CCNA_03716 (+0.56, FDR 0.005). 2
The same proteome found CCNA_01226 (lptC2) protein at +1.08 log2 in 4672/4659, with a net change of +0.66 log2 versus wild type, and CCNA_01217 at +0.77 versus 4659 or +0.74 versus wild type; these single-replicate observations are consistent with post-transcriptional stabilization but do not establish it statistically. 2
Pal/CCNA_00784 increased by +2.84 at the protein level and +2.08 at the transcript level, while several division and peptidoglycan-remodeling proteins decreased, including PbpC at -1.15 and membrane-bound transglycosylase A at -2.47 log2. 2
Evidence from respiratory_chain_wiring
Proteomics supports a passive, flux-based interpretation of condition-specific respiratory-chain wiring in acinetobacter-baylyi-adp1, rather than contradicting the existing use of protein abundance as complementary evidence. Under standard growth conditions, Complex I, NDH-2, and ACIAD3522 had similar protein levels: Complex I mean 27.6 at the 66th percentile, NDH-2 27.0 at the 59th percentile, and ACIAD3522 26.2 at the 48th percentile, compared with a genome median of 26.4; the spread was 1.4 units. 3
NDH-2 was therefore not repressed and was constitutively co-expressed with Complex I, while gene-phenotype data showed condition-specific respiratory requirements; together these observations support a model in which the limiting dehydrogenase depends on carbon-source-generated NADH flux rather than an active transcriptional switch. 3
This result refines the prior recommendation to combine FBA, fitness, and proteomics: abundance measurements can indicate that respiratory alternatives are present simultaneously, whereas growth-optimized FBA may predict zero flux through NDH-2 and ACIAD3522 because it preferentially routes NADH through the higher-ATP-yielding Complex I. 3
Interpretation limits
The expression values were averaged across 7 Acinetobacter strains rather than measured only in the exact knockout assay condition, so the association with essentiality is independent supporting evidence rather than a condition-matched causal test. 1
The report recommends combining FBA, fitness, and proteomics for essentiality prediction, but this proposed integration remains a recommended analysis rather than a completed result in the document. 1
The Caulobacter outer-membrane proteome had a single replicate per strain, so no per-protein statistics were available; the LptD/LptE decline, lptC2 induction, Pal-Tol upregulation, and CCNA_01217 increase require replicated proteomics. 2
The respiratory-chain protein measurements were made under standard growth conditions and do not directly establish carbon-source-specific abundance changes or measured flux distributions; the flux-based wiring interpretation remains partly inferential. 3
Related pages
- gene-essentiality — Proteomic expression was evaluated as a continuous predictor of knockout essentiality. 1
- multi-omics-integration — Proteomics was compared with FBA, TnSeq, knockout, and growth evidence, and later exposed transcript–protein discordance in envelope remodeling; respiratory-chain proteomics further supports integrating abundance with fitness and model outputs. 1,2,3
- Triple Essentiality Concordance Analysis for *Acinetobacter baylyi* ADP1 — Source summary for the triple-essentiality concordance analysis.
- Regulatory and proteomic architecture of Δfur-permitted lipid A loss in *Caulobacter crescentus* — Source summary for the Caulobacter Fur/lipid A-loss multi-omics analysis. 2
- Condition-Specific Respiratory Chain Wiring in ADP1 — Source summary for condition-specific respiratory-chain wiring in ADP1. 3