MS Amanda

MS Amanda is a scoring system to identify peptides out of tandem mass spectrometry data using a database of known proteins.

Downloads for 9 PD versions
PD3.1
MSAmanda_PD3.1_3.1.21.532.exe 522.4 KB · 2024-02-01 SHA-256 78e1163261a3e2976c3d0a0945ea8abfe357125bd018b00f5e4286cb721125a8
SHA-25678e1163261a3e2976c3d0a0945ea8abfe357125bd018b00f5e4286cb721125a8
MD5c8496ff34535d465de75b172812a8894

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD3.1_3.1.21.532.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.1_3.1.21.532.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '78e1163261a3e2976c3d0a0945ea8abfe357125bd018b00f5e4286cb721125a8') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD3.1_3.1.21.532.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.1_3.1.21.532.exe' && echo '78e1163261a3e2976c3d0a0945ea8abfe357125bd018b00f5e4286cb721125a8  MSAmanda_PD3.1_3.1.21.532.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD3.1_3.1.21.532.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.1_3.1.21.532.exe' && echo '78e1163261a3e2976c3d0a0945ea8abfe357125bd018b00f5e4286cb721125a8  MSAmanda_PD3.1_3.1.21.532.exe' | shasum -a 256 -c -
PD3.0
MSAmanda_PD3.0_3.0.20.558.exe 491.6 KB · 2022-10-18 SHA-256 f14425dcf6243632901a7cdb655ac5098d9ca19c170d8e3c346f11cb8b1da52d
SHA-256f14425dcf6243632901a7cdb655ac5098d9ca19c170d8e3c346f11cb8b1da52d
MD54d1c2a52b8eb250865eea2c41eab4b54

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD3.0_3.0.20.558.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.0_3.0.20.558.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'f14425dcf6243632901a7cdb655ac5098d9ca19c170d8e3c346f11cb8b1da52d') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD3.0_3.0.20.558.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.0_3.0.20.558.exe' && echo 'f14425dcf6243632901a7cdb655ac5098d9ca19c170d8e3c346f11cb8b1da52d  MSAmanda_PD3.0_3.0.20.558.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD3.0_3.0.20.558.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD3.0_3.0.20.558.exe' && echo 'f14425dcf6243632901a7cdb655ac5098d9ca19c170d8e3c346f11cb8b1da52d  MSAmanda_PD3.0_3.0.20.558.exe' | shasum -a 256 -c -
PD2.5
MSAmanda_PD2.5_2.5.20.566.exe 389.8 KB · 2022-10-25 SHA-256 15b4d23309317295adddbe877e2c2066f34a13e13e900cc2d7534fb6890f230d
SHA-25615b4d23309317295adddbe877e2c2066f34a13e13e900cc2d7534fb6890f230d
MD5afb94f3052218d3f741d6a2e20ae0bb3

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD2.5_2.5.20.566.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.5_2.5.20.566.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '15b4d23309317295adddbe877e2c2066f34a13e13e900cc2d7534fb6890f230d') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD2.5_2.5.20.566.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.5_2.5.20.566.exe' && echo '15b4d23309317295adddbe877e2c2066f34a13e13e900cc2d7534fb6890f230d  MSAmanda_PD2.5_2.5.20.566.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD2.5_2.5.20.566.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.5_2.5.20.566.exe' && echo '15b4d23309317295adddbe877e2c2066f34a13e13e900cc2d7534fb6890f230d  MSAmanda_PD2.5_2.5.20.566.exe' | shasum -a 256 -c -
PD2.4
MSAmanda_PD2.4_2.4.0.17952.exe 378.2 KB · 2021-03-18 SHA-256 df2b0015ac44d9d382c425f7426b4f093900982dc1bbff0ae10070dc703dcdc0
SHA-256df2b0015ac44d9d382c425f7426b4f093900982dc1bbff0ae10070dc703dcdc0
MD58eb77450f112be9ffff19b6121c57ca4

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD2.4_2.4.0.17952.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.4_2.4.0.17952.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'df2b0015ac44d9d382c425f7426b4f093900982dc1bbff0ae10070dc703dcdc0') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD2.4_2.4.0.17952.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.4_2.4.0.17952.exe' && echo 'df2b0015ac44d9d382c425f7426b4f093900982dc1bbff0ae10070dc703dcdc0  MSAmanda_PD2.4_2.4.0.17952.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD2.4_2.4.0.17952.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.4_2.4.0.17952.exe' && echo 'df2b0015ac44d9d382c425f7426b4f093900982dc1bbff0ae10070dc703dcdc0  MSAmanda_PD2.4_2.4.0.17952.exe' | shasum -a 256 -c -
PD2.3
MSAmanda_PD2.3.0.13282.exe 374.8 KB · 2019-09-20 SHA-256 3fae0dfef1832627816f8d044786a34e93a5c195f2fc90acdfeb5ada3d248baa
SHA-2563fae0dfef1832627816f8d044786a34e93a5c195f2fc90acdfeb5ada3d248baa
MD580a8f178438db42d5391751844cea338

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD2.3.0.13282.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.3.0.13282.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '3fae0dfef1832627816f8d044786a34e93a5c195f2fc90acdfeb5ada3d248baa') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD2.3.0.13282.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.3.0.13282.exe' && echo '3fae0dfef1832627816f8d044786a34e93a5c195f2fc90acdfeb5ada3d248baa  MSAmanda_PD2.3.0.13282.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD2.3.0.13282.exe' 'https://ms.imp.ac.at/data/msamanda/MSAmanda_PD2.3.0.13282.exe' && echo '3fae0dfef1832627816f8d044786a34e93a5c195f2fc90acdfeb5ada3d248baa  MSAmanda_PD2.3.0.13282.exe' | shasum -a 256 -c -
PD2.2
MSAmanda2.0_PD2.2_2.2.6.9691.zip 81.1 KB · 2017-12-21 SHA-256 1061f4019d1c035e8186fdd62e2cac94f948679745ab1226f08b14f26c65debf
SHA-2561061f4019d1c035e8186fdd62e2cac94f948679745ab1226f08b14f26c65debf
MD58b965113e6dd55230b01c4aefbc2ad25

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda2.0_PD2.2_2.2.6.9691.zip'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/MSAmanda2.0_PD2.2_2.2.6.9691.zip' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '1061f4019d1c035e8186fdd62e2cac94f948679745ab1226f08b14f26c65debf') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda2.0_PD2.2_2.2.6.9691.zip' 'https://ms.imp.ac.at/data/MSAmanda2.0_PD2.2_2.2.6.9691.zip' && echo '1061f4019d1c035e8186fdd62e2cac94f948679745ab1226f08b14f26c65debf  MSAmanda2.0_PD2.2_2.2.6.9691.zip' | sha256sum -c -
curl -fL -o 'MSAmanda2.0_PD2.2_2.2.6.9691.zip' 'https://ms.imp.ac.at/data/MSAmanda2.0_PD2.2_2.2.6.9691.zip' && echo '1061f4019d1c035e8186fdd62e2cac94f948679745ab1226f08b14f26c65debf  MSAmanda2.0_PD2.2_2.2.6.9691.zip' | shasum -a 256 -c -
PD2.1
MSAmanda_PD2.1.exe 370.9 KB · 2018-06-28 SHA-256 642e5f9b71d8a05429cf53abb250aff673ca8a799c8b7fc56b409c64f38a784b
SHA-256642e5f9b71d8a05429cf53abb250aff673ca8a799c8b7fc56b409c64f38a784b
MD561b98b74ddf2c6c820c511ffe63976b2

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD2.1.exe'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/MSAmanda_PD2.1.exe' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '642e5f9b71d8a05429cf53abb250aff673ca8a799c8b7fc56b409c64f38a784b') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD2.1.exe' 'https://ms.imp.ac.at/data/MSAmanda_PD2.1.exe' && echo '642e5f9b71d8a05429cf53abb250aff673ca8a799c8b7fc56b409c64f38a784b  MSAmanda_PD2.1.exe' | sha256sum -c -
curl -fL -o 'MSAmanda_PD2.1.exe' 'https://ms.imp.ac.at/data/MSAmanda_PD2.1.exe' && echo '642e5f9b71d8a05429cf53abb250aff673ca8a799c8b7fc56b409c64f38a784b  MSAmanda_PD2.1.exe' | shasum -a 256 -c -
PD1.4
MSAmanda_PD1.4_1.4.14.3866.zip 64.4 KB · 2017-09-19 SHA-256 d84bf2d5fea11a2508cf202ee6b3bc2b84ac07d9ce1f3c7293104332fa3f2bd9
SHA-256d84bf2d5fea11a2508cf202ee6b3bc2b84ac07d9ce1f3c7293104332fa3f2bd9
MD5a7e70e950e0dec9178f95b433864e3bb

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda_PD1.4_1.4.14.3866.zip'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/MSAmanda_PD1.4_1.4.14.3866.zip' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq 'd84bf2d5fea11a2508cf202ee6b3bc2b84ac07d9ce1f3c7293104332fa3f2bd9') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda_PD1.4_1.4.14.3866.zip' 'https://ms.imp.ac.at/data/MSAmanda_PD1.4_1.4.14.3866.zip' && echo 'd84bf2d5fea11a2508cf202ee6b3bc2b84ac07d9ce1f3c7293104332fa3f2bd9  MSAmanda_PD1.4_1.4.14.3866.zip' | sha256sum -c -
curl -fL -o 'MSAmanda_PD1.4_1.4.14.3866.zip' 'https://ms.imp.ac.at/data/MSAmanda_PD1.4_1.4.14.3866.zip' && echo 'd84bf2d5fea11a2508cf202ee6b3bc2b84ac07d9ce1f3c7293104332fa3f2bd9  MSAmanda_PD1.4_1.4.14.3866.zip' | shasum -a 256 -c -
PD1.3
MSAmanda1.3.4.1909.zip 52 KB · 2017-09-19 SHA-256 18a91e1eae8de5fa93046e4d7b814871fe4ebf1d8e32210581d1ea7d04317afd
SHA-25618a91e1eae8de5fa93046e4d7b814871fe4ebf1d8e32210581d1ea7d04317afd
MD5259a7814c04855ece1a90c26e6729f26

Downloads the file and checks its SHA-256; a click selects a whole checksum or command.

$ProgressPreference = 'SilentlyContinue'; $f = 'MSAmanda1.3.4.1909.zip'; Invoke-WebRequest -Uri 'https://ms.imp.ac.at/data/MSAmanda1.3.4.1909.zip' -OutFile $f; if ((Get-FileHash $f -Algorithm SHA256).Hash -eq '18a91e1eae8de5fa93046e4d7b814871fe4ebf1d8e32210581d1ea7d04317afd') { "OK: $f" } else { Remove-Item $f; Write-Error 'Checksum mismatch, file deleted' }
curl -fL -o 'MSAmanda1.3.4.1909.zip' 'https://ms.imp.ac.at/data/MSAmanda1.3.4.1909.zip' && echo '18a91e1eae8de5fa93046e4d7b814871fe4ebf1d8e32210581d1ea7d04317afd  MSAmanda1.3.4.1909.zip' | sha256sum -c -
curl -fL -o 'MSAmanda1.3.4.1909.zip' 'https://ms.imp.ac.at/data/MSAmanda1.3.4.1909.zip' && echo '18a91e1eae8de5fa93046e4d7b814871fe4ebf1d8e32210581d1ea7d04317afd  MSAmanda1.3.4.1909.zip' | shasum -a 256 -c -

Not supported: PD2.0, PD3.2, PD3.3.

About

This algorithm is especially designed for high resolution and high accuracy tandem mass spectra. One advantage of MS Amanda is the high speed of spectrum identification, especially since MS Amanda 2.0. In addition, MS Amanda is also very accurate, as we observe a high overlap of identified spectra with gold-standard algorithms Mascot and SEQUEST.
Since MS Amanda 3.0 automatic validation using Percolator can be performed.

More information about the implementation of MS Amanda and how the MS Amanda algorithm works is given here:

Installation of all versions of MS Amanda (Standalone and Proteome Discoverer Nodes)

Please download the latest version of MS Amanda from the The MS Amanda GitHub repository

Additional Information

In addition, MS Amanda Standalone is also integrated in SearchGUI and PeptideShaker!

A detailed description on how to use MS Amanda for Proteome Discoverer, on the parameters provided by MS Amanda, and how to filter results obtained with MS Amanda can be found in the MS Amanda Manual for PD.

A typical MS Amanda PD workflow can be found here.

Contact

This research project is a collaboration of the Protein Chemistry Group at IMP and the Bioinformatics Research Group at FH Upper Austria, Hagenberg Campus.
For any further questions, bug reports, ideas,... please contact Viktoria Dorfer, Marina Strobl, Stephan Winkler, or Karl Mechtler, or open an issue in the The MS Amanda GitHub repository, or post your comment in the MS Amanda Google Group.