Unrestrictive protein modification localization and quality control for open search of mass spectra

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br

The comparisons between our method and the <i>k</i>-medoid method on karate and football networks, where <i>λ</i> = 1.1, <i>β</i> = 1/<<i>k</i>>.

<p>Each data point is obtained by averaging over 100000 independent runs.</p

The spreader identification process of our method.

<p>(a) A toy network with 10 nodes and 3 super-nodes; (b) two spreaders identified by our method.</p

The growth ratio on three real networks for three centrality indices.

<p>The growth ratio on three real networks for three centrality indices.</p

The coverage ratios on three synthetic networks.

<p>The coverage ratios on three synthetic networks.</p

Loss of IRAK-1 causes decreased expression of <i>Lcn2</i> mRNA and protein <i>in vivo</i>.

<p>WT and IRAK-1^−/− C57/BL/6 female mice of 12 weeks old (6 each) were intraperitoneally injected with either 30 mg/kg of LPS or PBS for 6 hours. (A) Kidney tissues were extracted and subject to RNA extraction. <i>Lcn2</i> transcripts were measured by qRT-PCR assays and standardized against their respective controls (mice receiving PBS injections). Data is depicted as three separate mice (both WT and IRAK-1^−/−). *<i>P</i><0.05 (B) Protein lysates were extracted from the kidney tissues and subjected to Western blot. Blots were analyzed using LCN2 specific antibodies. The same blot was probed with β-actin as a loading control.</p

The influence scope with different proportions of spreader on three synthetic networks, where <i>λ</i> = 1.5, <i>β</i> = 1/<<i>k</i>>.

<p>Each data point is obtained by averaging over 200 independent runs.</p

The grow ratios on three synthetic networks.

<p>The grow ratios on three synthetic networks.</p

LPS stimulation induces a persistent induction of LCN2 in kidney fibroblasts.

<p>(A) LPS (100 ng/ml) induces a transient induction of <i>Tnfα</i> mRNA. (B) LPS (100 ng/ml) induces a persistent induction of <i>Lcn2</i> mRNA Transcript levels were measured by qRT-PCR as described above. The results are expressed as means +/− standard deviation performed in triplicate. (C) LCN2 protein levels persist after 24 hours of LPS stimulation. The levels of LCN2 were visualized by western blot.</p

Computational simulation captures the dynamic features of the experimental data.

<p>(A) The network motif responsible for the transient induction of <i>Tnfα</i> and the persistent induction of <i>Lcn2</i>. (B) Computational simulation of the transient induction of <i>Tnfα</i> and persistent induction of <i>Lcn2</i>. Circles denote actual experimental data. Lines represent computational simulations.</p