SpliceVista is a bioinformatic tool which enables splice variants analysis and visualization in shotgun proteomics.
More than 90% of human genes have alternatively spliced products, gene centric analysis omits differential regulation of splice variants. Illustrated in the above figure.
(Red peptides are Isoform A specific peptides, black ones are shared between two isoforms)
Published in Mol. Cell Proteomics 2014 Jun;13(6):1552-62
Download at Github https://github.com/yafeng/SpliceVista/
PQPQ is an algorithm to cluster peptides identified in mass spectrometry based their quantitative pattern across samples.
Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ). Forshed et al.
Mol Cell Proteomics. 2011 Oct. http://www.ncbi.nlm.nih.gov/pubmed/21734112
Download at Github for python version. https://github.com/yafeng/pqpq_python