piDeepNet is a Deep Neural Network regression prediction algorithm for determining the isoelectrict point (pI) of HiRief compatible peptides. This tool allows you to calculate the pI based for non-modified and singly phosphorylated peptides.
 
 
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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.

Reference:

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