Shimadzu Introduces Software Solutions for its AXIMA™ line of Mass Spectrometers

Shimadzu Scientific Instruments introduces three new software products, designed to complement the Shimadzu Biotech AXIMA™ line of MALDI mass spectrometer — QC Reporter™, PTM Finder™ and SeqLab™.

QC Reporter™ software, when used with one of the AXIMA MALDI TOF instruments, provides a complete solution to the mass spectrometric quality control (QC) needs of modern chemical manufacturing facilities. It is a fully automated platform designed for high-throughput quality control of synthetic products using MALDI TOF MS. It operates on a newly developed software platform called MALDI Solutions™. QC Reporter is application-centric software written, in close collaboration with customers, with the actual QC workflow in mind. It facilitates the whole process from the preparation bench to the final reporting. The software user interface is designed to only display relevant information and functions to the task being performed and provide an intuitive user experience with a quick and painless learning curve to end-users. The software runs on Microsoft Windows Vista, Windows XP Professional or Windows Server 2003 and uses SQL Server 2008.

With QC Reporter software running on an AXIMA MALDI mass spectrometer, a very large number of independent samples can be lined up for automatic analysis on a single plate. Analysis of each individual sample is very quick, making this solution ideal for high-throughput labs. Running costs of MALDI analysis are very low, while a large variety of samples can be run choosing the right combination of matrix and ionic charge modes. Finally, MALDI makes for simple spectral interpretation with singly charged peaks, has good relative quantification reproducibility and has very low probability of producing false positive results.

PTM Finder™ software facilitates the identification of post-translational modifications in complex protein samples, including interrogating data for hypothetical, novel modifications using MS/MS data. It also allows users to find peptide sequences carrying one or more modifications using MS/MS data. The software facilitates consecutive Mascot searches using all the functionality of the MS/MS Ion Search. Peptides that do not match any proteins during the searches can be directed towards a “PTM Define” module where users can define their own, hypothetical modifications and screen the remaining MS/MS data for specific shifts in fragment masses, neutral losses and/or diagnostic ions. Such searches are quick and thorough, as they are performed based on a reduced database of protein sequences. The software is designed to allow the user to easily import amino acid sequences using a simple copy/paste function or use the proteins derived from the initial Mascot search results, giving the user the flexibility to search for PTMs whether or not they know the protein they are working with.

SeqLab™ de-novo sequencing software uses a high-power de-novo sequencing engine and allows the use of MS/MS and possible related MS/MS/MS data to help decipher peptide sequences. The use of MS/MS data can give high-quality de-novo sequences and tags for peptides from low- or high-energy CID MS/MS data, including data from the AXIMA Performance, Shimadzu Biotech’s TOFTOF.

SeqLab’s unique power is fully realized in combination with the AXIMA Resonance, the newly launched MALDI QIT TOF mass spectrometer from Shimadzu Biotech. The AXIMA Resonance can provide very high mass accuracy tandem mass spectrometric data, which enhance the success of de-novo sequencing. Additionally, SeqLab can make use of related MS/MS/MS data, which provide more information, and complete the sequence across the length of the peptide.