:: DESCRIPTION
BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Using BiblioSpec for creating and searching tandem MS peptide libraries.
Frewen B, MacCoss MJ.
Curr Protoc Bioinformatics. 2007 Dec;Chapter 13:Unit 13.7.
:: DESCRIPTION
Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.
::DEVELOPER
Proteomics & Integrative Bioinformatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Proteomics. 2011 Apr;11(7):1340-5. doi: 10.1002/pmic.201000650. Epub 2011 Feb 17.
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Fermin D, Basrur V, Yocum AK, Nesvizhskii AI.
:: DESCRIPTION
EagleEye removes background MS/MS spectra by comparing them with a non-annotated collection of spectra, obtained from combined LC-MS/MS runs of control in-gel digests as well as identified in on-going proteomis projects.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Junqueira, M., Spirin, V., Balbuena, T. S., Waridel, P., Surendranath, V., Kryukov, G., Adzhubei, I., Thomas, H., Sunyaev, S. and Shevchenko, A.
Separating the wheat from the chaff: unbiased filtering of background tandem mass spectra improves protein identification.
J Proteome Res. 2008 Aug;7(8):3382-95. Epub 2008 Jun 18.
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragments and generates a list of probable candidate structures.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SimLipid is a comprehensive informatics tool for characterizing lipids using precursors and product ions data from MS, MS/MS and MSE data.
Lipidomics is an emerging field of systems biology being applied to disease research, drug discovery and biomarker identification. Mass spectrometry is one of the most sophisticated technologies for identification and quantification of lipids from biological mixtures. However, the major challenge in mass spectrometric data analysis is the huge amount of data generated in the process. Some of the most important aspects of mass spectrometric lipidome data analysis are the high throughput quantitative analysis of crude lipid extracts and structural identification of lipids using precursor and product ion data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MascotDatfile is an open-source library to fully parse and analyse MASCOT MS/MS search results.
::DEVELOPER
Computational Omics and Systems Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Helsens et al.
MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results.
Proteomics (2007) vol. 7 (3) pp. 364-6
:: DESCRIPTION
X!TandemPipeline is a free software that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.
::DEVELOPER
pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The Peptizer platform was created to automate the manual validation process by an expert system. The user can create a rule set via by enabling a set of Agent objects that will each inspect an assumption based on expert knowledge. Subsequent aggregation of multiple Agent inspection the enables separation of peptide identifications by these rules.
::DEVELOPER
Computational Omics and Systems Biology Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Helsens et al.
Peptizer: A tool for assessing false positive peptide identifications and manually validating selected results.
Molecular & cellular proteomics : MCP (2008) vol. 7 (12) pp. 2363-72.
:: DESCRIPTION
Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proteomics. 2010 Mar;10(5):1087-90.
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.
Barsnes H, Eidhammer I, Martens L.
