:: DESCRIPTION
ProMS (Proteome Analysis using Mass Spectrometry) is a Web Server for Validation and Manipulation of Mass Spectrometry-based Proteomics data.
::DEVELOPER
Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
DiagnoProt is a tool that finds discriminative mass spectra among different biological conditions and ultimately performs spectral profiling classification of unknown conditions by comparing sets of tandem mass spectra (MS/MS).
::DEVELOPER
Laboratory for Computational and Strucutural Proteomics – Fiocruz
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Silva ARF, Lima DB, Leyva A, Duran R, Batthyany C, Aquino PF, Leal JC, Rodriguez JE, Domont GB, Santos MDM, Chamot-Rooke J, Barbosa VC, Carvalho PC.
DiagnoProt: a tool for discovery of new molecules by mass spectrometry.
Bioinformatics. 2017 Jun 15;33(12):1883-1885. doi: 10.1093/bioinformatics/btx093. PMID: 28186229.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semi-quantitative data from raw data files, which allows for more rapid biological insight.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Broeckling CD, Reddy IR, Duran AL,Zhao X and Sumner LW.
MET-IDEA: data extraction tool for mass spectrometry-based metabolomics.
Anal Chem. 2006 Jul 1;78(13):4334-41.
:: 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
:: DOWNLOAD
:: 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.
:: 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
MSBLAST is a specialised BLAST –based protocol developed for identification of proteins by sequence similarity searches using peptide sequences produced by the interpretation of tandem mass spectra.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Anal Chem. 2001 May 1;73(9):1917-26.
Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG.
:: DESCRIPTION
IDEAL-Q is an automated analysis tool for label-free quantitative proteomics. It accepts mzXML raw data format and Mascot xml and ProtXML/PepXML for identification result. IDEAL-Q uses an elution time prediction and peak alignment algorithms to quantify peptides across different LC-MS runs and increase quantitation coverage. Furthermore, the tool adopts an stringent validation step on Signal-to-noise ratio, Charge state, Isotopic distribution (SCI validation) to ensure quantitation accuracy. IDEAL-Q provides variously optional normalization tools for flexible workflow design such as addition of fractionation strategies and multiple spiked internal standards
::DEVELOPER
Computational Omics Labortary, Academia Sinica
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chih-Chiang Tsou et al. ,
“IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation”,
Molecular & Cellular Proteomics, Vol. 9, pp. 131-144, 2010.
:: 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.