Skip to main content

Advertisement

Table 1 Selected open access software tools in proteomics

From: Cardiovascular proteomics in the era of big data: experimental and computational advances

Open access tools Language/framework License Publication Website
Database search engine (untargeted proteomics)
Comet*,† C++ Apache 2.0 [93] [94]
MS-GF+*,† Java Custom/Academic [31] [95]
MSAmanda C#/Mono Custom/Academic [96] [97]
ProLuCID*,† Java Custom/Academic [26] [98]
X!Tandem*,† C++ OSI Artistic [99] [100]
Targeted proteomics and/or data-independent acquisition
Skyline* C# Apache 2.0 [101] [102]
OpenSWATH*,† C++ BSD 3-Clause [103] [104]
Protein inference and/or search post-processing
Percolator*,† C++ Apache 2.0 [34] [105]
ProteinProphet*,† C++ GNU LGPLv2 [106] [107]
ProteinInferencer Java Custom/Academic [35] [98]
Protein quantification
MaxQuant .NET Custom/Academic [108] [109]
Census Java Custom/Academic [110] [98]
PLGEM*,† R GNU GPLv2 [111] [112]
QPROT*,† C GNU GPLv3 [37] [113]
Pipelines and toolkits
Perseus .NET Custom/Academic [114] [115]
Crux* C++ Apache 2.0 [116] [105]
OpenMS* C++ BSD 3-Clause [117] [118]
TPP* C++ GNU LGPLv2 [119] [120]
Data access and reuse
PeptideShaker* Java Apache 2.0 [121] [122]
PRIDE inspector* Java Apache 2.0 [123] [124]
  1. Proteomics software tools that provide open access to users. Many of these tools are also open source which potentially allows users to participate in the continual development of the tools
  2. * Available open-source source code repository at the time of writing
  3. Platform-independent (Windows, Linux, Mac)