:: DESCRIPTION
ProteoSAFe is a Proteomics Environment which is Scalable in utilizing distributed computing, Accessible via reconfigurable, easy-to-learn user interfaces, and Flexible in tool chaining.
::DEVELOPER
To-ju Huang (t3huang@ucsd.edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Inspect is a general purpose database search algorithm, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, Inspect implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.
::DEVELOPER
Natalie Castellana [ncastell(at)cs.ucsd.edu]
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
InsPecT: Fast and accurate identification of post-translationally modified peptides from tandem mass spectra.
Stephen Tanner, Hongjun Shu, Ari Frank, Ling-Chi Wang, Ebrahim Zandi, Marc Mumby, Pavel A. Pevzner, and Vineet Bafna.
Anal Chem. 2005 Jul 15;77(14):4626-39
:: DESCRIPTION
pFind Studio is a computational solution for mass spectrometry-based proteomics. pFind Studio includes pFind, pBuild, pLabel, pXtract, pParse and pScan
pXtract creates .DTA .MGF and .MS2 input files directly from Thermo Scientific .raw LC-MS/MS data files.
pParse is a software dedicated to recalibrate the monoisotopic of precursors in MS/MS spectra datasets assigned by mass spectrometry
pFind is a search engine for peptide and protein identification via tandem mass spectrometry.
pNovo+ is a de novo peptide sequencing algorithm using complementary HCD and ETD tandem mass spectra.
pBuild is a tool that can compare several search engines’ results and combine them together. The latest version, pBuild v2.0, can process the search results of pFind, SEQUEST and Mascot.
pQuant is the software for quantitative proteomics, evaluates the accuracy of caluculated peptide and protein ratios.
pLabel is a spectra labeling tool that can visualize the global- and local-view peptide-spectrum matches, given the results of pFind or any other search engines. pLabel can label both CID and ETD spectra, and implement the manual de novo sequencing.
pLink is a software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry.
pScan is a flexible tool that helps biologists to preprocess protein sequence databases in proteomics research.
pCluster is a software tool aiming at detecting protein modifications independent of sequence databases by tandem mass spectral clustering.
pMatch is a spectral library search tool, which is deliberately designed for the open search mode.
::DEVELOPER
Bioinformatics group, Institute of Computing Technology, Chinese Academy of Sciences
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rapid Communications in Mass Spectrometry, 21,2985-2991,2007.
pFind 2.0: a software package for peptide and protein identification via tandem mass spectrometry.
Le-Heng Wang, De-Quan Li, Yan Fu, Hai-Peng Wang, Jing-Fen Zhang, Zuo-Fei Yuan,Rui-Xiang Sun, Rong Zeng, Si-Min He, Wen Gao.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
F. Liu et al., (2010)
ProHits: an integrated software platform for mass spectrometry-based interaction proteomics.
Nat Biotech, 28:1015-7
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
