ProteoCombiner v1.0 – Integrating Top-down, Bottom-up and Middle-down Proteomics data

ProteoCombiner v1.0

:: DESCRIPTION

ProteoCombiner capitalizes on the data arising from different experiments and proteomics search engines and presents the results in a user-friendly manner. Our tool also provides a rapid and easy visualization, manual validation and comparison of the identified proteoform sequences, including post-translational modifications (PTM) characterization.

::DEVELOPER

MSBIO – INSTITUT PASTEUR

:: SCREENSHOTS

:: REQUIREMENTS

Windows
The .NET framework

:: DOWNLOAD

ProteoCombiner

:: MORE INFORMATION

Citation

Lima DB, Dupré M, Duchateau M, Gianetto QG, Rey M, Matondo M, Chamot-Rooke J.
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment.
Bioinformatics. 2021 Aug 9;37(15):2206-2208. doi: 10.1093/bioinformatics/btaa958. PMID: 33165572.

TDFragMapper 1.0 – Visualization tool for Evaluating Experimental parameters in top-down Proteomics

TDFragMapper 1.0

:: DESCRIPTION

TDFragMapper can deal with multiple fragmentation methods and can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics.

::DEVELOPER

MSBIO – INSTITUT PASTEUR

:: SCREENSHOTS

:: REQUIREMENTS

Windows
The .NET framework

:: DOWNLOAD

TDFragMapper

:: MORE INFORMATION

Citation

Dhenin J, Lima DB, Dupré M, Chamot-Rooke J.
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics.
Bioinformatics. 2021 Nov 18:btab784. doi: 10.1093/bioinformatics/btab784. Epub ahead of print. PMID: 34792554.

PatternLab for proteomics V – tool for analyzing Shotgun Proteomic data

PatternLab for proteomics V

:: DESCRIPTION

PatternLab for proteomics is a one-stop shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins/peptides that are differentially expressed and those that are unique to a state. It can also cluster the ones that share similar expression profiles in time-course experiments, as well as help in interpreting results according to Gene Ontology.

::DEVELOPER

Laboratory for Computational and Strucutural Proteomics – Fiocruz

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

PatternLab for proteomics

:: MORE INFORMATION

Citation

Paulo C. Carvalho, John R. Yates III, Valmir C. Barbosa
Analyzing Shotgun Proteomic Data with PatternLab for Proteomics
Current Protocols in Bioinformatics Unit 13.13 DOI: 10.1002/0471250953.bi1313s30

DIAproteomics 1.2.4 – Automated Quantitative Analysis of DIA Proteomics Mass Spectrometry Measurements

DIAproteomics 1.2.4

:: DESCRIPTION

diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

::DEVELOPER

the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Docker

:: DOWNLOAD

DIAproteomics

:: MORE INFORMATION

Citation

Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H.
DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics.
J Proteome Res. 2021 Jul 2;20(7):3758-3766. doi: 10.1021/acs.jproteome.1c00123. Epub 2021 Jun 21. PMID: 34153189.

VESPA 1.1.1 – Visual Analytics Platform for Exploring Proteogenomics data

VESPA 1.1.1

:: DESCRIPTION

VESPA (Visual Exploration and Statistics to Promote Annotation) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.

::DEVELOPER

Computational Biology & Bioinformatics, Pacific Northwest National Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

VESPA

:: MORE INFORMATION

Citation

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.
BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

Topograph 2 – Precursor Enrichment corrected global Protein Turnover Measurements

Topograph 2

:: DESCRIPTION

Topograph is an advanced program for the analysis of proteomics data using stable isotope labeling.

::DEVELOPER

MacCoss Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

Topograph

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2012 Nov;11(11):1468-74. doi: 10.1074/mcp.O112.017699. Epub 2012 Aug 3.
Topograph, a software platform for precursor enrichment corrected global protein turnover measurements.
Hsieh EJ1, Shulman NJ, Dai DF, Vincow ES, Karunadharma PP, Pallanck L, Rabinovitch PS, MacCoss MJ.

Cromwell 1.0 – The New Model Processor for Mass Spectrometry Data

Cromwell 1.0

:: DESCRIPTION

Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell represents our third attempt (at least) to find a method to process spectra that both works quickly and achieves reasonably good results.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Matlab

:: DOWNLOAD

Cromwell

:: MORE INFORMATION

Citation

Cancer Inform. 2005;1:41-52.
Understanding the characteristics of mass spectrometry data through the use of simulation.
Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R.

NeoFlow – Proteogenomics Pipeline for Neoantigen discovery

NeoFlow

:: DESCRIPTION

NeoFlow is a streamlined computational workflow that integrates WES and MS/MS proteomics data for neoantigen prioritization to facilitate cancer immunotherapy.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
R
Python

:: DOWNLOAD

NeoFlow

:: MORE INFORMATION

Citation

Wen B, Li K, Zhang Y, Zhang B.
Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.
Nat Commun. 2020 Apr 9;11(1):1759. doi: 10.1038/s41467-020-15456-w. PMID: 32273506; PMCID: PMC7145864.

DeepRescore – Rescore PSMs leveraging Deep Learning-derived Peptide Features

DeepRescore

:: DESCRIPTION

DeepRescore is an immunopeptidomics data analysis tool that leverages deep learning-derived peptide features to rescore peptide-spectrum matches (PSMs).

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

DeepRescore

:: MORE INFORMATION

Citation

Li K, Jain A, Malovannaya A, Wen B, Zhang B.
DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics.
Proteomics. 2020 Nov;20(21-22):e1900334. doi: 10.1002/pmic.201900334. Epub 2020 Sep 27. PMID: 32864883; PMCID: PMC7718998.

PTM-Shepherd v1.1.1 – A tool for Summarizing Open Search Results

PTM-Shepherd v1.1.1

:: DESCRIPTION

PTM-Shepherd automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PTM-Shepherd

:: MORE INFORMATION

Citation

Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI.
PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.
Mol Cell Proteomics. 2020 Dec 11;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub ahead of print. PMID: 33568339; PMCID: PMC7950090.