2008/11/10 by Sharon Gauci, Bas van Breukelen, Simone Lemeer +2 · 3 citations
Chemistry · Biochemistry, Genetics and Molecular Biology · #Advanced Proteomics Techniques and Applications #Mass Spectrometry Techniques and Applications #Machine Learning in Bioinformatics
paper · doi:10.1002/pmic.200800295
openalex publication_date 2008/11/10 · openalex created_date 2016/06/24 · openalex updated_date 2026/05/21
We experimentally demonstrate the use of an in-house developed pI calculator which takes into account peptide PTM such as phosphorylation and N-terminal acetylation. The pI calculator was utilized for a large set of peptides derived from a complex zebrafish lysate fractionated using peptide IEF, whereby a good correlation between the calculated (theoretical) pI and the experimental pI could be established. This pI calculator permits the implementation of optimal pK values depending on the experimental conditions and a reliable calculation of peptide pI which can be utilized as a filtering technique in validating peptide identifications. Our data reveal that the shift due to a phosphorylation or N-terminal acetylation is highly dependent on the presence of acidic or basic residues in the peptide. Furthermore, using this pI calculator, we revealed previously unknown position-specific pKs of asparagine and carbamidomethylated cysteine depending on their location in the peptide. Collectively, this peptide pI calculator is a welcome addition to the versatility and robustness of IEF for the separation and confident identification of (post-translationally modified) peptides.