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Pro-ker Proteomics Analysis

Version: 4.10.1

Publisher: Billy M Ngo

Published: April 2026

Updated: April 2026

Ngo, B.M. (2026). Pro-ker Proteomics Analysis [Software].

References & Acknowledgments

D3.js — Data visualization library

MaxQuant — Proteomics data processing

Benjamini & Hochberg (1995) — FDR correction method

Tusher, Tibshirani & Chu (2001) — SAM / S0 fudge factor

Tyanova et al. (2016) — Perseus computational platform

Statistical Methods

Volcano Plot — Differential Expression

Welch’s t-test — Two-sample unequal-variance t-test comparing group means. Degrees of freedom estimated via the Welch–Satterthwaite equation. P-values are computed from the regularized incomplete beta function.

Benjamini–Hochberg FDR — Multiple-testing correction controlling the false discovery rate. Adjusted p-values (q-values) are computed by ranking raw p-values and scaling by n/rank.

S0 correction — A fudge factor added to the t-test denominator (SE + S0) to penalize fold changes driven by low-abundance noise (Tusher et al., 2001). At S0 = 0 this is a standard t-test. Typical values range from 0.1–2.0.

Missing value imputation — Four methods available:
• Perseus-style Gaussian (default): draws from a down-shifted normal distribution in log2 space (shift=1.8 SD, width=0.3 SD). Ref: Tyanova et al. (2016) Nature Protocols 11:2301.
• MinProb: draws from a Gaussian centered at the 1st percentile of the log2 distribution. Ref: Lazar et al. (2016) J. Proteome Res. 15:1116.
• kNN: imputes from k=10 nearest neighbor proteins by Euclidean distance. Ref: Troyanskaya et al. (2001) Bioinformatics 17:520.
• Min/2: replaces with half the minimum non-zero value (simple deterministic baseline).
Reproducibility: Perseus and MinProb draw random values, but each protein gets a deterministic seed derived from the user-supplied Random seed (default 42) and the protein's filtered index, computed as (seed·1000003 + 2·fi + 1or2) mod 2³². Same seed + same data → identical imputed values and an identical volcano plot. Change the seed to verify a conclusion is robust to the specific draws — a result that depends on a single seed is not robust. The seed is recorded on the Volcano Settings sheet of the XLSX export.

Log2 Fold Change — Calculated as log2(mean_X / mean_Y). Positive values indicate higher abundance in Group X; negative values indicate higher abundance in Group Y.

PCA — Principal Component Analysis

Algorithm — Dual-space PCA (kernel method) optimized for datasets where the number of samples is much smaller than the number of features. Computes the n×n kernel matrix K = X·X^T from the mean-centered data matrix, then performs Jacobi eigendecomposition.

Scores — PC scores are eigenvectors scaled by the square root of their eigenvalues. Variance explained is reported as a percentage of total variance for each component.

Version History

4.1.0 (April 2026)
+Shape annotations (rectangle, circle, diamond, triangle with color/fill/border), two-row toolbar with editing controls below, separate volcano FC/FDR threshold line toggles, canvas panning by click-drag on empty space

4.0.0 (April 2026)
Published imputation methods (Perseus, MinProb, kNN), robust session save/load with graph positions and annotations, searchable protein dropdown with FASTA drag-drop for coverage map, amino acid-level peptide display with boundary markers, context menu color swatch, UI tooltips, upload performance fix

3.9.0 (April 2026)
Protein Abundance ranked plot with error bars (SD, SEM, range), volcano tooltip guidance for FC threshold and S0

3.8.0 (April 2026)
Unified color swatch palette across all pickers, swatch popup toolbar fix, dynamic macOS plist version

3.7.0 (April 2026)
Fix canvas text/line annotation glitches, unified default marker size, auto-shutdown lock path fix, merge all pending features

3.6.0 (April 2026)
Groups of Interest, species highlight, 2-of-diamonds logo, hover shows protein ID, min click target, toolbar enhancements, color swatch on hover, remove Bokeh

3.5.0 (April 2026)
Peptide coverage map (FASTA sequence input, residue-level visualization), desktop icon fix

3.4.0 (April 2026)
Volcano threshold lines & group side labels, S0 low-abundance correction, volcano/PCA data in CSV export, statistical methods documentation, README

3.3.0 (April 2026)
BiNgo color swatches, undo/redo, hollow markers, resizable panels, volcano fixes

3.2.0 (March 2026)
Intra-group dot plots, toolbar annotations, PCA fix, dot plot axis breaks

3.1.0 (March 2026)
Number inputs for graph settings, centered plots, scroll zoom

3.0.0 (March 2026)
Custom ProkerChart SVG engine (replaces Plotly), context toolbar, canvas zoom

2.9.0 (March 2026)
Beeswarm unique plot, radio aggregation, freeze graphs

2.8.0 (March 2026)
Dynamic version, rebuilt tutorial, transparent backgrounds

2.7.0 (March 2026)
Fix color selection, clean labels, draggable plots

2.6.0 (February 2026)
Comprehensive CSV export

2.5.0 (February 2026)
Export Canvas (SVG/PNG), text boxes, lines, grid toggle

2.4.0 (February 2026)
Arial font, improved visual quality, ProkerChart SVG engine

2.3.0 (February 2026)
Fix axis/title editing

2.2.0 (February 2026)
Editable titles/axes, right-click selection

2.1.0 (February 2026)
Graph settings, click-to-label, intensity toggle, axis editing

2.0.0 (February 2026)
BiNgo-style header, info panel, themes, session save, auto-update, desktop shortcut