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.

ProHits v4.0.3 – LIMS for Interaction Proteomics.

ProHits v4.0.3

:: DESCRIPTION

ProHits is an open source software package designed to help scientists store, search and analyze mass spectrometry data, in particular for protein-protein interaction experiments.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

ProHits

:: REQUIREMENTS

  • Linux
  • PHP
  • Apache
  • MYSQL.

:: DOWNLOAD

 ProHits

:: MORE INFORMATION

Citation:

F. Liu et al., (2010)
ProHits: an integrated software platform for mass spectrometry-based interaction proteomics.
Nat Biotech, 28:1015-7

Philosopher 4.0.0 – Toolkit for Shotgun Proteomics data analysis

Philosopher 4.0.0

:: DESCRIPTION

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Philosopher

:: MORE INFORMATION

Citation

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI.
Philosopher: a versatile toolkit for shotgun proteomics data analysis.
Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

MSFragger / FragPipe 16.0 – Peptide Identification in Mass Spectrometry-based Proteomics

MSFragger / FragPipe 16.0

:: DESCRIPTION

MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

FragPipe is a Java Graphical User Interface (GUI) for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger – an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

MSFragger / FragPipe

:: MORE INFORMATION

Citation:

Andy Kong, Felipe Leprevost, Dmitry Avtonomov, Dattatreya Mellacheruvu, Alexey Nesvizhskii.
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics
Nat Meth, May 2017. DOI: 10.1038/nmeth.4256

DIA-Umpire 2.2.2 – Computational Analysis pipeline for DIA Proteomics data

DIA-Umpire 2.2.2

:: DESCRIPTION

DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 DIA-Umpire

:: MORE INFORMATION

Citation:

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.
Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.
Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255.

ProtMAX – Analyzing Large Shotgun Proteomics Mass Spectrometry data sets

ProtMAX

:: DESCRIPTION

ProtMAX is a fast and robust software tool for analyzing large shotgun proteomics mass spectrometry data sets.

::DEVELOPER

Molecular Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ProtMAX

:: MORE INFORMATION

Citation:

Nat Protoc. 2013 Mar;8(3):595-601. doi: 10.1038/nprot.2013.013. Epub 2013 Feb 28.
Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments.
Egelhofer V1, Hoehenwarter W, Lyon D, Weckwerth W, Wienkoop S.

LFQuant 20120114 – Label-free Quantitative Analysis Tool for LC-MS/MS Proteomics Data

LFQuant 20120114

:: DESCRIPTION

LFQuant is a new analysis tool for label-free LC-MS/MS quantitative proteomics data. It is compatible with high-resolution mass spectrometers (Thermo RAW data) and two popular database search engines (SEQUEST and MASCOT) with target-decoy search strategy.

::DEVELOPER

LFQuant team

:: SCREENSHOTS

LFQuant

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LFQuant

:: MORE INFORMATION

Citation

Proteomics. 2012 Dec;12(23-24):3475-84. doi: 10.1002/pmic.201200017.
LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.
Zhang W1, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H.

aLFQ 1.3.6 – Estimating Absolute Protein Quantities from Label-free LC-MS/MS Proteomics data

aLFQ 1.3.6

:: DESCRIPTION

aLFQ is a bioinformatics tool which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.

::DEVELOPER

aLFQ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 aLFQ

:: MORE INFORMATION

Citation

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.
Rosenberger G, Ludwig C, Röst HL, Aebersold R, Malmström L.
Bioinformatics. 2014 Sep 1;30(17):2511-3. doi: 10.1093/bioinformatics/btu200.

OpenMS / pyOpenMS 2.6.0 – C++ / Python Framework for Proteomics

OpenMS / pyOpenMS 2.6.0

:: DESCRIPTION

OpenMS is an open-source software C++ library for LC/MS data management and analyses. It offers an infrastructure for the development of mass spectrometry related software.

pyOpenMS provides Python-bindings for the C++ OpenMS mass spectrometric algorithm library, allowing researchers to directly access algorithms and data structures available in C++ from the interactive Python environment. pyOpenMS thus provides access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis, giving the user functionality ranging from file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).

DEVELOPER

OpenMS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows  / MacOsX
  • C++ Compiler / Python

:: DOWNLOAD

 OpenMS / pyOpenMS

:: MORE INFORMATION

Citation:

Röst HL, Schmitt U, Aebersold R, Malmström L.
pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.
Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246. PMID: 24420968.

TOPPAS: A Graphical Workflow Editor for the Analysis of High-Throughput Proteomics Data.
Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.
J Proteome Res. 2012 Jul 6;11(7):3914-20. Epub 2012 May 24.

OpenMS and TOPP: open source software for LC-MS data analysis.
Bertsch A, Gröpl C, Reinert K, Kohlbacher O.
Methods Mol Biol. 2011;696:353-67.