Bioinformatics Services

Full Data Analysis Support for Discovery and Targeted Services: The facility offers comprehensive data analysis with all proteomics services, including normalization, differential expression analysis, and preparation of interactive figures including heat maps and volcano plots. High-resolution, publication-quality figures are provided for manuscripts and grant proposals. Further details can be found below.

Mascot and MaxQuant Database Searches: Proteins and peptides are identified and quantified by matching MS/MS spectra to database entries for any biological species with a sequenced genome. Post-translational modifications can also be included in search parameters. Quantitative results can be reported as spectral counts, peptide peak intensities, or TMT reporter ions.

proteiNorm: We have developed in-house software for quality testing, filtering of peptides/proteins, testing various normalization methods, and performing differential analysis directly from database search results. proteiNorm has four major functions: (1) filtering options to remove outlier samples and low quality proteins/peptides, (2) normalization methods are tested quantitatively and qualitatively, (3) batch effects are identified and removed, (4) differential analysis is performed using the most appropriate statistical method.

ProteoViz: To facilitate the process of interpreting statistical results form phosphor-proteomics studies, we have developed in-house software for exploration of processed data. Following data acquisition, ProteoViz performs data preprocessing, differential analysis, pathway and gene set enrichment analysis, identifies motifs and kinases, and provides visualization of all the results using an interactive dashboard. The protein analysis function can also be applied to label-free protein quantification.

PTMViz: For analysis of histone PTMs, we have developed in-house software that allows a user to upload histone PTM intensity values and perform quality control, normalization, differential expression, and visualization. An interactive dashboard allows users to filter samples and sample groups so they can visualize only a subset of data or plot a data distribution before and after normalization to evaluate different methods. The normalized data can then be visualized using interactive heatmaps, volcano plots, boxplots, and bar plots of histone PTMs.

Targeted Analysis: Full bioinformatics support is provided for PRM, SRM, and targeted assays described in the sections above. Data are analyzed using Skyline and in-house R scripts, and peak areas for each transition are summed to generate quantitative intensity values for each sample. The calculated intensity values can then be loaded into the in-house software described above for visualization.