Tag Archives: Proteogenomics

Utilizing RNA-Seq data to improve proteomics

rna-seq

Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene ...

Read More »

Splicify – a proteogenomic pipeline to detect differentially expressed protein isoforms based on integrating RNA-Seq and Mass Spec data

rna-seq

Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, ...

Read More »

Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy Reveals Human Proteomic Variation

Mass spectrometry-based proteomic analysis underestimates proteomic variation due to the absence of variant peptides and posttranslational modifications (PTMs) from standard protein databases. Each individual carries thousands of missense mutations that lead to single amino acid variants, but these are missed ...

Read More »