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] |