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) […]

Isoelectric point calculation of native proteins

The isoelectric point (pI) of native (not denaturated) proteins is important in several separation techniques. The pI is defined as the pH value at which the positive and negative charges on the protein are balanced and the net charge is zero. To determine the pH at which the net charge is zero, the charge on […]

Encrypted data transfer enabled on Prot pi

To protect your valuable data, Prot pi is now reachable via HTTPS with secure sockets layer (SSL) encryption. Therefore the protpi.ch domain was migrated to a server with a static IP address and a security certificate was issued. The reason for this is to keep your sensitive information sent across the internet encrypted so that […]

MALDI-TOF-MS analysis of antibody-antigen complexes

Editor: Prof. Dr. Christiane Zaborosch Head of Center for Biochemistry Lecturer in Biochemistry christiane.zaborosch@zhaw.ch  Introduction In the development of new drugs, it is of interest in pharmaceutical research to determine the size of antibody-antigen complexes that have formed, since it is assumed that large complexes are cleared more quickly by the body, and thus the […]