Table 1 Selected open access software tools in proteomics

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]