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  1. Recipe for generating proteotypic peptides for example database
  2. ReleasePlanning
  3. Respect your Results
  4. Running the TPP Singularity image
  5. Running the TPP docker image
  6. Scheduling on regis cluster
  7. SearchProteins
  8. Software:ASAPRatio
  9. Software:CompassXport
  10. Software:Corra
  11. Software:Cytoscape
  12. Software:DidIScanThat
  13. Software:Firegoose, Gaggle, and PIPE
  14. Software:JRAP
  15. Software:Libra
  16. Software:MZIdentML
  17. Software:Mascot2XML
  18. Software:Mayu
  19. Software:MsXML2Other
  20. Software:MzXML2Search
  21. Software:Out2Summary
  22. Software:Out2XML
  23. Software:Overview
  24. Software:Pep3D
  25. Software:PepXMLViewer
  26. Software:PeptideAtlas
  27. Software:PeptideProphet
  28. Software:PeptideSieve
  29. Software:PeptideSieve:Build
  30. Software:PeptideSieve:Builld
  31. Software:PeptideSieveRetrainingTurtorial
  32. Software:Petunia
  33. Software:Prequips
  34. Software:Prequips:Inclusion List Builder
  35. Software:ProbID
  36. Software:ProteinProphet
  37. Software:QualScore
  38. Software:RAMP
  39. Software:RAP
  40. Software:ReAdW
  41. Software:RemoteConvert
  42. Software:SBEAMS
  43. Software:SPE
  44. Software:SWATHProphet
  45. Software:SpecArray
  46. Software:SpectraST
  47. Software:StPeter
  48. Software:SubsetDB
  49. Software:SuperHirn
  50. Software:TIQAM
  51. Software:TPP
  52. Software:TPP-MaRiMba
  53. Software:TPP:EC2
  54. Software:Tandem2XML
  55. Software:Tomcat
  56. Software:XLink
  57. Software:XPRESS
  58. Software:da2tpp
  59. Software:massWolf
  60. Software:msBID
  61. Software:mzBruker
  62. Software:mzStar
  63. Software:mzWiff
  64. Software:pkl2mzXML
  65. Software:readmzXML
  66. Software:trapper
  67. Spectra assignment
  68. Spectrast.params
  69. Spectrast.usermods
  70. Spectrast create.params
  71. TPP:4.1 Release Notes
  72. TPP:4.2.0 Release Notes
  73. TPP:4.2.1 Release Notes
  74. TPP:4.3.0 Release Notes
  75. TPP:4.4.0 Release Notes
  76. TPP:4.4.1 Release Notes
  77. TPP:4.5.0 Release Notes
  78. TPP:4.5.0 SVN Log
  79. TPP:4.5.1 Release Notes
  80. TPP:4.5.1 SVN Log
  81. TPP:4.5.2 Release Notes
  82. TPP:4.5.2 SVN Log
  83. TPP:4.6.0 Release Notes
  84. TPP:4.6.0 SVN Log
  85. TPP:4.6.1 Release Notes
  86. TPP:4.6.1 SVN Log
  87. TPP:4.6.2 Release Notes
  88. TPP:4.6.2 SVN Log
  89. TPP:4.6.3 Release Notes
  90. TPP:4.6.3 SVN Log
  91. TPP:4.7.0 Release Notes
  92. TPP:4.7.0 SVN Log
  93. TPP:4.7.1 Release Notes
  94. TPP:4.7.1 SVN Log
  95. TPP:4.8.0 Release Notes
  96. TPP:4.8.0 SVN Log
  97. TPP:5.0.0 Release Notes
  98. TPP:5.0.0 SVN Log
  99. TPP:5.0 Installation
  100. TPP:5.1.0 Release Notes
  101. TPP:5.1.0 SVN Log
  102. TPP:5.1 Installation
  103. TPP:5.2.0 Release Notes
  104. TPP:5.2.0 SVN Log
  105. TPP:5.2 Installation
  106. TPP:6.0.0 Release Notes
  107. TPP:6.1.0 Release Notes
  108. TPP:6.2.0 Release Notes
  109. TPP:6.3.0 Release Notes
  110. TPP:7.0.0 Release Notes
  111. TPP:Authors and Contributors
  112. TPP:Building Windows-native binaries with Mingw
  113. TPP:Building Windows-native binaries with Visual Studio 2005
  114. TPP:Cloud
  115. TPP:Developer Documentation
  116. TPP:Directory Layout
  117. TPP:Documentation
  118. TPP:Example data analysis
  119. TPP:Files and Formats
  120. TPP:Frequently Asked Questions
  121. TPP:Getting the sourcecode for a windows build
  122. TPP:Installing on Mac OSX
  123. TPP:Installing on Ubuntu 7.04
  124. TPP:Installing on Ubuntu 8.10
  125. TPP:Installing the Trans-Proteomic Pipeline (TPP) 4.4.0 on Mac OS X 10.6.4
  126. TPP:Mascot and the TPP
  127. TPP:NovorIntegration
  128. TPP:Phenyx and the TPP
  129. TPP:ProbID and the TPP
  130. TPP:Related Tools
  131. TPP:Sequest and the TPP
  132. TPP:Supported Search Engines
  133. TPP:Using Petunia
  134. TPP:V5Feedback
  135. TPP:V5Tasks
  136. TPP:Windows Cygwin Installation
  137. TPP:X!Tandem and the TPP
  138. TPPDev:Branching
  139. TPPDev:ReleaseChecklist
  140. TPP 4.2.1: Installing on Ubuntu 9.04
  141. TPP 4.3.1: Installing on Ubuntu 10.04
  142. TPP 4.5.2: Installing on Ubuntu 10.04.3
  143. TPP 5.0.0: Installing on Ubuntu 16.04
  144. TPP 5.1.0: Installing on Ubuntu 16.04 LTS
  145. TPP 5.2.0: Installing on Ubuntu 18.04 LTS
  146. TPP 5.x development: Installing on Ubuntu 16.04
  147. TPP 6.0.0: Installing on Ubuntu 20.04 LTS
  148. TPP 6.1.0: Installing on Ubuntu 20.04 LTS
  149. TPP 6.2.0: Installing on Ubuntu 22.04 LTS
  150. TPP 7.0.0: Installing on Ubuntu 22.04 LTS
  151. TPP AMI 4.6.2 README
  152. TPP AMI 4.6.3 README
  153. TPP AMI 4.7.0 README
  154. TPP AMI 4.7.1 README
  155. TPP AMI 4.8.0 README
  156. TPP AMZTPP
  157. TPP AMZTPP:PetuniaTutorial
  158. TPP Amazon Machine Images
  159. TPP SEWW Demo2012
  160. TPP TWA
  161. TPP TWA:Tutorial
  162. TPP Tandem search
  163. TPP Tutorial
  164. TPP Tutorial v1
  165. TPP Tutorial v2
  166. TPP Tutorials
  167. TPP WISB Demo2012
  168. TPP testimonials
  169. Terry's blog
  170. Terry's compbio links
  171. Tutorial:StPeter1
  172. Using SBEAMS
  173. Using mProphet at ISB
  174. Windows Installation Guide

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