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  1. AMZTPP:FAQ
  2. Alt NxST search strategy
  3. Bash/tcsh syntax differences
  4. Building Peptide Atlas
  5. Citing the TPP
  6. ComputationalPredictionofProteotypicPeptides
  7. Custom digest site
  8. Debugging:CGI programs
  9. Debugging:Understanding XSL-Generating Code in Perl
  10. Debugging:Working with boost::shared ptr
  11. Developer: Boost CPP libraries
  12. Expert search and TPP usage
  13. Export questions discussion list
  14. FetchDataset
  15. Formats:Overview
  16. Formats:mzXML
  17. Formats:pepXML
  18. Formats:protXML
  19. GetProteinAPI
  20. GetProteinsAPI
  21. GetTransitionsAPI
  22. Glyco-peptide
  23. Glyco-peptide TODO list
  24. Installing and building TPP on Windows
  25. Link
  26. Links on mindfulness, meditation, and Buddhism
  27. Linux Installation Guides
  28. MS level 2
  29. Main Page
  30. Mayu
  31. Ms/ms
  32. Msconvert Capabilities
  33. Msconvert Wine
  34. My new page
  35. NewFrontPage
  36. NewGlycoPage
  37. PABST
  38. PABST peptide examples
  39. PeptideAtlas:Chromosomal coverage
  40. PeptideAtlas Pipeline Retool 2012/13
  41. PeptideAtlas software
  42. PeptideSieveRetrainingTutorial
  43. Prequips:Bugs
  44. Prequips:Documentation
  45. Prequips:Eclipse Setup
  46. Prequips:FAQ
  47. Prequips:Wishlist
  48. Processing glycopeptide data
  49. Protein identification terminology
  50. Raw MS file conversion
  51. Recipe for generating proteotypic peptides for example database
  52. ReleasePlanning
  53. Respect your Results
  54. Running the TPP Singularity image
  55. Running the TPP docker image
  56. Scheduling on regis cluster
  57. SearchProteins
  58. Software:ASAPRatio
  59. Software:CompassXport
  60. Software:Corra
  61. Software:Cytoscape
  62. Software:DidIScanThat
  63. Software:Firegoose, Gaggle, and PIPE
  64. Software:JRAP
  65. Software:Libra
  66. Software:MZIdentML
  67. Software:Mascot2XML
  68. Software:Mayu
  69. Software:MsXML2Other
  70. Software:MzXML2Search
  71. Software:Out2Summary
  72. Software:Out2XML
  73. Software:Overview
  74. Software:Pep3D
  75. Software:PepXMLViewer
  76. Software:PeptideAtlas
  77. Software:PeptideProphet
  78. Software:PeptideSieve
  79. Software:PeptideSieve:Build
  80. Software:PeptideSieve:Builld
  81. Software:PeptideSieveRetrainingTurtorial
  82. Software:Petunia
  83. Software:Prequips
  84. Software:Prequips:Inclusion List Builder
  85. Software:ProbID
  86. Software:ProteinProphet
  87. Software:QualScore
  88. Software:RAMP
  89. Software:RAP
  90. Software:ReAdW
  91. Software:RemoteConvert
  92. Software:SBEAMS
  93. Software:SPE
  94. Software:SWATHProphet
  95. Software:SpecArray
  96. Software:SpectraST
  97. Software:StPeter
  98. Software:SubsetDB
  99. Software:SuperHirn
  100. Software:TIQAM
  101. Software:TPP
  102. Software:TPP-MaRiMba
  103. Software:TPP:EC2
  104. Software:Tandem2XML
  105. Software:Tomcat
  106. Software:XLink
  107. Software:XPRESS
  108. Software:da2tpp
  109. Software:massWolf
  110. Software:msBID
  111. Software:mzBruker
  112. Software:mzStar
  113. Software:mzWiff
  114. Software:pkl2mzXML
  115. Software:readmzXML
  116. Software:trapper
  117. Spectra assignment
  118. Spectrast.params
  119. Spectrast.usermods
  120. Spectrast create.params
  121. TPP:4.1 Release Notes
  122. TPP:4.2.0 Release Notes
  123. TPP:4.2.1 Release Notes
  124. TPP:4.3.0 Release Notes
  125. TPP:4.4.0 Release Notes
  126. TPP:4.4.1 Release Notes
  127. TPP:4.5.0 Release Notes
  128. TPP:4.5.0 SVN Log
  129. TPP:4.5.1 Release Notes
  130. TPP:4.5.1 SVN Log
  131. TPP:4.5.2 Release Notes
  132. TPP:4.5.2 SVN Log
  133. TPP:4.6.0 Release Notes
  134. TPP:4.6.0 SVN Log
  135. TPP:4.6.1 Release Notes
  136. TPP:4.6.1 SVN Log
  137. TPP:4.6.2 Release Notes
  138. TPP:4.6.2 SVN Log
  139. TPP:4.6.3 Release Notes
  140. TPP:4.6.3 SVN Log
  141. TPP:4.7.0 Release Notes
  142. TPP:4.7.0 SVN Log
  143. TPP:4.7.1 Release Notes
  144. TPP:4.7.1 SVN Log
  145. TPP:4.8.0 Release Notes
  146. TPP:4.8.0 SVN Log
  147. TPP:5.0.0 Release Notes
  148. TPP:5.0.0 SVN Log
  149. TPP:5.0 Installation
  150. TPP:5.1.0 Release Notes
  151. TPP:5.1.0 SVN Log
  152. TPP:5.1 Installation
  153. TPP:5.2.0 Release Notes
  154. TPP:5.2.0 SVN Log
  155. TPP:5.2 Installation
  156. TPP:6.0.0 Release Notes
  157. TPP:6.1.0 Release Notes
  158. TPP:6.2.0 Release Notes
  159. TPP:6.3.0 Release Notes
  160. TPP:7.0.0 Release Notes
  161. TPP:Authors and Contributors
  162. TPP:Building Windows-native binaries with Mingw
  163. TPP:Building Windows-native binaries with Visual Studio 2005
  164. TPP:Cloud
  165. TPP:Developer Documentation
  166. TPP:Directory Layout
  167. TPP:Documentation
  168. TPP:Example data analysis
  169. TPP:Files and Formats
  170. TPP:Frequently Asked Questions
  171. TPP:Getting the sourcecode for a windows build
  172. TPP:Installing on Mac OSX
  173. TPP:Installing on Ubuntu 7.04
  174. TPP:Installing on Ubuntu 8.10
  175. TPP:Installing the Trans-Proteomic Pipeline (TPP) 4.4.0 on Mac OS X 10.6.4
  176. TPP:Mascot and the TPP
  177. TPP:NovorIntegration
  178. TPP:Phenyx and the TPP
  179. TPP:ProbID and the TPP
  180. TPP:Related Tools
  181. TPP:Sequest and the TPP
  182. TPP:Supported Search Engines
  183. TPP:Using Petunia
  184. TPP:V5Feedback
  185. TPP:V5Tasks
  186. TPP:Windows Cygwin Installation
  187. TPP:X!Tandem and the TPP
  188. TPPDev:Branching
  189. TPPDev:ReleaseChecklist
  190. TPP 4.2.1: Installing on Ubuntu 9.04
  191. TPP 4.3.1: Installing on Ubuntu 10.04
  192. TPP 4.5.2: Installing on Ubuntu 10.04.3
  193. TPP 5.0.0: Installing on Ubuntu 16.04
  194. TPP 5.1.0: Installing on Ubuntu 16.04 LTS
  195. TPP 5.2.0: Installing on Ubuntu 18.04 LTS
  196. TPP 5.x development: Installing on Ubuntu 16.04
  197. TPP 6.0.0: Installing on Ubuntu 20.04 LTS
  198. TPP 6.1.0: Installing on Ubuntu 20.04 LTS
  199. TPP 6.2.0: Installing on Ubuntu 22.04 LTS
  200. TPP 7.0.0: Installing on Ubuntu 22.04 LTS
  201. TPP AMI 4.6.2 README
  202. TPP AMI 4.6.3 README
  203. TPP AMI 4.7.0 README
  204. TPP AMI 4.7.1 README
  205. TPP AMI 4.8.0 README
  206. TPP AMZTPP
  207. TPP AMZTPP:PetuniaTutorial
  208. TPP Amazon Machine Images
  209. TPP SEWW Demo2012
  210. TPP TWA
  211. TPP TWA:Tutorial
  212. TPP Tandem search
  213. TPP Tutorial
  214. TPP Tutorial v1
  215. TPP Tutorial v2
  216. TPP Tutorials
  217. TPP WISB Demo2012
  218. TPP testimonials
  219. Terry's blog
  220. Terry's compbio links
  221. Tutorial:StPeter1
  222. Using SBEAMS
  223. Using mProphet at ISB
  224. Windows Installation Guide

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