Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and has undergone several rounds of annotation. University of Liverpool researchers...
Read More »Your transcript assembly method is affecting downstream proteomics results
Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames ...
Read More »Utilizing RNA-Seq data to improve proteomics
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 »Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data
The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled ...
Read More »Splicify – a proteogenomic pipeline to detect differentially expressed protein isoforms based on integrating RNA-Seq and Mass Spec data
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 »Proteome profiling outperforms transcriptome profiling for co-expression based gene function prediction
Co-expression of mRNAs under multiple conditions is commonly used to infer co-functionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; ...
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 »Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing
Mass spectrometry-based methods allow for the direct, comprehensive analysis of expressed proteins and their quantification among different conditions. However, in general identification of proteins by assigning experimental mass spectra to peptide sequences of proteins relies on matching mass spectra to ...
Read More »MSProGene – integrative proteogenomics beyond six-frames and single nucleotide polymorphisms
Ongoing advances in high-throughput technologies have facilitated accurate proteomic measurements and provide a wealth of information on genomic and transcript level. In proteogenomics, this multi-omics data is combined to analyze unannotated organisms and to allow more accurate sample-specific predictions. Existing ...
Read More »PGTools – a software suite for proteogenomics data analysis and visualization
Researchers from the Queensland Centre for Medical Genomics have developed PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools is comprised of applications, libraries, customized databases and visualization tools for analysis of mass-spectrometry data using ...
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