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Casio SMF Converter lets you convert SMF files to formats for Casio instruments.

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Trans Proteomics Pipeline
 Institute for Systems Biology  16  Freeware
It can be used for statistical validation of peptide and protein identification.
Pattern Lab for Proteomics
 pattern recognition software  14  Demo
Efficient and panoptic software to addresses shotgun proteomic data analysis.
Progenesis QI for proteomics
 Nonlinear Dynamics  34  Demo
Progenesis QI for proteomics is discovery analysis software for your LC-MS data.
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Secure My Files
5  SecuSimple  138  Shareware
Encrypt and decrypt files with this extremely well-crafted program.
GenePattern
 Broad Institute, MIT  52  Freeware
GenePattern is a powerful genomic analysis platform.
ProteinID Finder
7  Proteome Solutions Inc.  Shareware
ProteinID Finder is a commercial protein analyzation program.
GeneSpringGX
2  Strand Life Sciences Pvt Ltd  37  Shareware
Agilent's GeneSpring GX provides powerful, accessible statistical tools.
Thermo Proteome Discoverer
6  Thermo Fisher Scientific Inc  152  Commercial
Proteome Discoverer software is a comprehensive tool for proteomic data analysis.
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Peaks Studio
2  Bioinformatics Solutions Inc.  82  Demo
PEAKS Studio offers a complete proteomics software.
Bruker Daltonics BioTools
2  Bruker Daltonik GmbH  65  Commercial
BioTools provides an unprecedented support to mass spectrometry-based proteomics.
Mass spectrometry - MSQuant
 Peter Mortensen  7  Open source
MSQuant is a tool for quantitative proteomics/mass spectrometry.
JVirGel
 Karsten Hiller  10  Freeware
JVirGel is a program for the simulation and analysis of proteomics data.
Insilicos Viewer
2  Insilicos LLC  29  Freeware
Insilicos Viewer is a free viewer for mass spectrometry proteomics data.
IDEAL-Q
1  IIS, Academia Sinica  4  Freeware
IDEAL-Q is an automated analysis tool for label-free quantitative proteomics.
Scaffold 3
 Proteome Software  Shareware
Scaffold - Visualize and Validate Complex MS/MS Proteomics Experiments.
ProteinLynx Global Server
2  Waters  24  Commercial
It is a platform for quantitative and qualitative proteomics research.
OpenMS
 OpenMS Developer Team  141  Freeware
OpenMS is an open source framework for LC-MS based proteomics.
pLabel
2  ICT  10  Freeware
pLabel is a mass spectral peak labeling software for proteomics research.
Non-reviewed
Informed-Proteomics
 Pacific Northwest National Laboratory  1