Software

In-House Software

Proteomics

Analytical Pipeline Software for MALDI In-Source Decay Mass Spectrometry Imaging.

How to cite : T. A. Zimmerman, D. Debois, G. Mazzucchelli, V. Bertrand, M. C. De Pauw-Gillet, E. De Pauw. “An Analytical Pipeline for MALDI In-Source Decay Mass Spectrometry Imaging of Proteins.” Anal. Chem., 2011, 83, 6090–6097. DOI:10.1021/ac201221h

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InkCompare: A Program For Statistical Comparisons of Inks Based on Mass Spectrometry Data

SequenceAssembly: A Program To Assemble Amino Acid Sequences of Entire Proteins

“Sequence Assembly” is a custom and free-to-use algorithm by Tyler A. Zimmerman. It is specifically dedicated to the assembly of de novo peptide candidates issued from the application of the Multi-Enzymatic Limited Digestion (MELD) methodology. The code is written in Java programming language. Program scheme, input formatting and “how to use” instructions are also provided.

Cleaning Mass Spectrometry Imaging Data by Selective Removal of MALDI Matrix Peaks

Physical Chemistry

ParsIMoS

ParsIMoS is free software (Apache open-source licensed) for high-throughput input conversion for theoretical CCS prediction calculations using IMoS. ParsIMoS allows for the rapid and efficient conversion of different MM, MD, and DFT calculation outputs into IMoS input files. ParsIMoS is especially thought out, with pre-encoded settings, for converting MobCal input and Gaussian output files to IMoS input files in its EXCEL format. ParsIMoS is capable of parsing multiple calculation outputs at the same time (with batch capability) to individual IMoS input files. It also allows converting outputs containing multiple structures (e.g. extracted from molecular dynamics simulations) into a single IMoS input file.

ParsIMoS is coded as cross-platform software (.exe for Windows 64-bit, .app for MacOS and a Unix executable file) in Lazarus v.1.6.2 (Free Pascal) with graphical user interface. ParsIMoS link : https://github.com/JeanRNH/ParsIMoS

How to cite : Kune, C., Haler, J., Far, J. and De Pauw, E. (2018), Effectiveness and limitations of computational chemistry and mass spectrometry in the rational design of target-specific shift reagents for ion mobility spectrometry. ChemPhysChem. DOI :10.1002/cphc.201800555