Amidation is one of the most common post-translational modification in which the C-terminal carboxyl group is replaced by an amide group1–5. Amidation plays an important role in peptidesand peptide hormones. More than half of all mammalian peptide hormones and more than 80 % of all insect hormones have amidated C-termini1. The mechanism of amidation is […]
Mass spectrum simulator in Prot pi version 2.2
A new mass spectrum simulator comes with the current version 2.2 of Prot pi. This simulator brings some weighty benefits such as to define the ion adduct, charge state and resolution. An awesome feature is the possibility to integrate multiple compounds in one mass spectrum. This gives amongst others the opportunity to simulate multiple charge state of a compound. In […]
A mass spectrometry imaging software: Quantinetix™
ImaBiotech, founded in 2009 by a team of experts, offers new molecular imaging (called MALDI imaging) services and products to life science industries. This new technology is capable of visualizing and quantifying biological compounds that play role in many pathologies like Cancer, Alzheimer or Parkinson diseases. It is also an interesting tool to follow new […]
Fast ultra-high resolution mass spectrum simulation with Prot pi version 2.1
Version 2.1 of the Protein Tool comes with a completely new software architecture. Even ultra-high resolution (up to 1’000’000) mass spectra of large proteins can now be simulated within sub-seconds. To get the mass spectrum, Prot pi calculates the accurate isotopic distribution using isotope-frequencies and mass defects of the chemical elements. Also the overall calculation time […]
Peptide Tool Released with Prot pi 2.0
We just released the version 2.0 of Prot pi which introduces the Peptide Tool, a brand new software architecture and many improvements for higher performance and stability. Prot pi | Peptide Tool brings a lot of useful features to analyse peptide sequences. Major improvements New Peptide Tool New software architecture Modification data base Minor improvements Several graphical […]
MS-based Glycan Analysis of the Glycoprotein Ricin
1 Background N-glycosylations affect important properties such as the specificity, efficacy, immunogenicity and stability of proteins. A portfolio of methods for glycan analysis was developed, using the murine monoclonal antibody 1RK1, an IgG1κ, to enable N-glycosylations of proteins to be analysed (Fig. 1). The methods developed were subsequently applied to the plant glycoprotein ricin.
Enhanced processing power for faster calculations
The new version 1.2.0.27 of Prot pi is released on 15 March 2015. In this version several computationally expensive procedures were optimized for more efficiency. The overall calculation time is now shortened by up to a factor of five. Major improvements Enhanced processing power and performance optimized algorithm enables faster calculations Optimized scroll behavior for mobile […]
Prediction of potential modification sites in proteins
Some sequence motifs in proteins tend to be modified. Thus, for example an N-terminal glutamine or glutamic acid residue can spontaneously lead to a cyclization. This reaction results in an N-terminal pyroglutamic acid with elimination of ammonia or water, respectively. Aspartyl and asparaginyl deamidation, isomerization, and racemization reactions can spontaneously occur, if the subsequent amino acid […]
Molecular mass and isoelectric point calculator for glycosylated proteins
Glycosylations should not be neglected for the correct calculation of the molecular mass, the isoelectric point and the mass-specific UV absorption coefficient. Therefore Prot pi provides a tool to draw glycans as a posttranslational modification of proteins. This short guide deals with how to add two complex-type N-Glycosylation G1 with a sialic acid (N-acetylneuraminic acid) […]
Calculation of glycosylated proteins enabled
A module to define N-glycosylation as a posttranslational modification of a Protein was implemented. Users of Prot pi | Protein Tool can draw glycan trees using Prot pi’s GlycoTree.js JavaScript plugin.