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

Increased ss-motif similiarity within miRNA families.

<p>The panels show the average number of common ss-motif among members of each miRNA family (arrow), compared to a distribution of average pre-miRNAs (repeated 1000 times). A. The miRNA gene family mir-515 (26 members; 172 common ss-motifs). B. The miRNA gene family mir-154 (17 members; 118 common ss-motifs). C. The miRNA gene family let-7 (8 members; 428 common ss-motifs).</p

Comparison between Mirident and previously published software/algorithms.

1<p>Original training data.</p>2<p>“Th” indicates “Threshold”.</p><p>All the models were tested on the same data set of 124 pre-miRNAs and 124 non-pre-miRNA hairpins.</p

Mirident performance.

<p>A. Effect of increasing number of ss-motifs on miRNA prediction accurracy. Note: The X-axis is discontinuous above 1500 motifs (dashed line). B. The ROC curve of Mirident (red line) trained with 1300 ss-motifs. The Area Under Curve (AUC) is 0.99. Results for other methods are shown for comparison.</p

Mirident prediction accuracy on non-human and novel pre-miRNA data sets.

<p>Mirident prediction accuracy on non-human and novel pre-miRNA data sets.</p

The Mirident pipeline.

<p>The Mirident pipeline.</p

Sequence-structure motif characteristics.

<p>Light hues (pink, light green) indicates the positive and negative randomly selected sequences (RSS). Darker hues (red, green) indicates the actual ss-motifs derived from the positive (pre-miRNA) and negative (CDS hairpin) training sets. A. Combinations of nucleotide and structural information in the ss-motifs. The figure shows occurrence of structural information relative to positions with specific nucleotide information. “Comb” denotes occurrences of specific nucleotide and structural information combined at the same position (<i>e.g.</i>, “A_L”, “C_D”, etc). “Up neighb” and “Dw neighb” denote occurrences of specific nucleotide notation combined with specific structural notations at the nearest upstream or downstream neighbouring position (<i>e.g.</i>, “N_LA_S” etc, and “A_SN_L” etc), respectively. B. Distribution of “L”, “R” and “D” denotes “left”, “right” and absence of (notation of) intramolecular interactions, respectively.</p