Software

Spectronaut™

https://biognosys.com/shop/spectronaut

This commercially available software package is used for the analysis of data-independent acquisition (DIA) proteomic experiments. It supports DIA data from any instrument platform and can quantitatively profile hundreds to thousands of proteins within one experiments. Larger experiments containing several conditions and replicates can also be analysed.

 

PEAKS

The software platform PEAKS Studio offers solutions for a wide spectrum of proteomic research questions. It may be used for protein identification and quantification, analysis of post-translational modifications, sequence variants and peptide/protein de novo sequencing. Protein quantification can be either performed label-based or label-free. Thus, the software also supports data-dependent (DDA) and data-independent acquisition and ion mobility analysis.

ISOQuant

http://www.immunologie.uni-mainz.de/isoquant/

ISOQuant is a software tool for processing label-free quantitative LC-MS/MS proteomics data.
It is designed for high throughput post-processing of (Waters ProteinLynx Global Server preprocessed) label-free LC-MS/MS data, that have been acquired using MSE, HDMSE and UDMSE data independent acquisition approaches.
As part of an academical project, ISOQuant is an open source software and freely available under conditions of a BSD-like license.

Reference:
Distler, U., Kuharev, J., Navarro, P., Levin, Y., Schild, H., & Tenzer, S. (2014). Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nature Methods, 11(2), 167–170. http://doi.org/10.1038/nmeth.2767

 

LFQbench

https://github.com/IFIproteomics/LFQbench

LFQbench is an open source R package for the automated evaluation of label-free quantification performance. The Evaluation is based on the interpretation of the quantitative analysis results of hybrid proteome samples prepared in known ratios.
LFQbench calculates and represents graphically a set of qualitative and quantitative performance metrics like identification rates, precision and accuracy of quantification, providing developers and end-users with a standardized set of reports to enable an in-depth performance evaluation of software and analytical platforms.

References:
[1] Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou C, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R & Tenzer S. A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology 1546-1696 (2016). DOI: 10.1038/nbt.3685
[2] Kuharev J, Navarro P, Distler U, Jahn O & Tenzer S. In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics 15, 3140–3151 (2015).

 

LFQbench2

https://github.com/MatteoLacki/LFQBench2

This Programme is the next generation of the LFQBench R package. LFQBench2 offers quick access to IsoQuant data and a simple way to prepare visualizations of your mass spectrometric benchmark.

Reference:
Distler, Ute, et al. "Enhancing Sensitivity of Microflow-Based Bottom-Up Proteomics through Postcolumn Solvent Addition." Analytical chemistry 91.12 (2019): 7510-7515.

 

IsoSpec2.0

https://github.com/MatteoLacki/IsoSpec

Developed together with the group of Computational Biology and Bioinformatics (chief developper, Dr. Michał Startek), IsoSpec2.0 is an algorithm used to simulate infinitely resolved mass distributions. The algorithm is available as a stand-alone C++ code, Python module, and R package. The algorithm is also included in the epic OpenMS platform.

Reference:
Łącki, Mateusz K., et al. "IsoSpec: Hyperfast fine structure calculator." Analytical chemistry 89.6 (2017): 3272-3277.

 

masstodon

https://github.com/MatteoLacki/masstodon

Masstodon is a software tool for analysing top-down proteomics experiments and, more generally, for any in-depth analysis of any in depth, custom-search analysis of a mass spectrum. The software is open source and coded in Python.

Reference:
Łącki, Mateusz Krzysztof, et al. "masstodon: A tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry." Analytical chemistry (2019), DOI: 10.1021/acs.analchem.8b01479

 

rta (in progress)

https://github.com/MatteoLacki/rta

Rta stands for retention time alignment. It is a Python code which provides a set of tools for calibrating retention times.

 

Efficient Data Storage and Access for TIMS-TOF IMS-DIA datasets

https://github.com/michalsta/opentims
https://github.com/MatteoLacki/timspy
https://github.com/MatteoLacki/timsr

In collaboration with Bruker and Dr. Michał Startek from the University of Warsaw we developed a collection of software tools called opentims, timspy and timsr for easy access to timsTOF data. These tools are free of charge.

Reference:
Łącki MK, Startek MP, Brehmer S, Distler U, Tenzer S. OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data. J Proteome Res. 2021 Mar 16. doi: 10.1021/acs.jproteome.0c00962. Epub ahead of print.

Editing software

Furious Fastas

https://github.com/MatteoLacki/furious_fastas

Furious Fastas is a simple Python module which can be used for downloading Fasta files from Uniprot, automatically updating the resulting sequence libraries, and translating sequences between different formats.