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1. Main Page (1,118,493 views)
2. Software:TPP (546,291 views)
3. TPP Tutorial v2 (532,513 views)
4. TPP Tutorial v1 (500,926 views)
5. Formats:mzXML (365,792 views)
6. Software:SpectraST (358,456 views)
7. TPP Tutorial (299,136 views)
8. Building Peptide Atlas (290,192 views)
9. TPP:Windows Cygwin Installation (230,629 views)
10. TPP:Installing on Mac OSX (213,949 views)
11. Software:ReAdW (205,935 views)
12. Terry's compbio links (199,370 views)
13. Msconvert Wine (196,625 views)
14. Windows Installation Guide (183,138 views)
15. ReleasePlanning (183,132 views)
16. Msconvert Capabilities (164,440 views)
17. TPP:Developer Documentation (158,631 views)
18. TPP Tandem search (152,168 views)
19. Software:SuperHirn (146,960 views)
20. TPP:V5Feedback (119,253 views)
21. TPP Amazon Machine Images (118,404 views)
22. Software:Overview (113,725 views)
23. TPP:4.5.1 Release Notes (109,994 views)
24. Software:massWolf (109,683 views)
25. Software:PeptideSieve (99,883 views)
26. TPP:Using Petunia (95,732 views)
27. TPP AMZTPP (94,148 views)
28. TPP:Frequently Asked Questions (91,570 views)
29. TPP:4.4.0 Release Notes (87,887 views)
30. TPP SEWW Demo2012 (87,314 views)
31. Formats:pepXML (85,209 views)
32. Software:RemoteConvert (80,152 views)
33. TPP:Cloud (78,449 views)
34. PeptideSieveRetrainingTutorial (74,686 views)
35. TPP:Installing the Trans-Proteomic Pipeline (TPP) 4.4.0 on Mac OS X 10.6.4 (74,113 views)
36. TPP:X!Tandem and the TPP (72,671 views)
37. TPP:Related Tools (71,880 views)
38. Software:TIQAM (64,680 views)
39. Software:mzStar (60,953 views)
40. Software:ProteinProphet (60,879 views)
41. TPP:Authors and Contributors (57,433 views)
42. Software:PeptideProphet (56,789 views)
43. TPP TWA:Tutorial (56,281 views)
44. Expert search and TPP usage (56,123 views)
45. Software:Libra (55,221 views)
46. Software:mzWiff (53,617 views)
47. PeptideAtlas:Chromosomal coverage (51,563 views)
48. PABST peptide examples (48,496 views)
49. Software:RAMP (48,345 views)
50. TPP:4.8.0 Release Notes (48,118 views)
51. TPP:4.7.0 Release Notes (48,073 views)
52. Software:MzXML2Search (47,409 views)
53. TPP:4.7.1 Release Notes (47,381 views)
54. Software:Prequips:Inclusion List Builder (47,360 views)
55. Software:ASAPRatio (46,449 views)
56. Terry's blog (46,148 views)
57. Prequips:Eclipse Setup (44,806 views)
58. Software:readmzXML (44,587 views)
59. Software:msBID (44,316 views)
60. Software:Pep3D (43,818 views)
61. TPP:4.6.2 Release Notes (43,606 views)
62. Software:mzBruker (43,303 views)
63. Software:trapper (42,425 views)
64. Software:TPP-MaRiMba (40,592 views)
65. Software:Firegoose, Gaggle, and PIPE (39,386 views)
66. TPP:Documentation (39,067 views)
67. TPP 4.5.2: Installing on Ubuntu 10.04.3 (37,943 views)
68. TPP:4.5.0 Release Notes (37,131 views)
69. Software:XPRESS (35,777 views)
70. Spectrast.params (35,382 views)
71. Running the TPP docker image (34,529 views)
72. TPP:Example data analysis (33,599 views)
73. TPP 5.2.0: Installing on Ubuntu 18.04 LTS (31,582 views)
74. TPP:Supported Search Engines (31,488 views)
75. TPP:4.6.3 Release Notes (30,979 views)
76. Software:CompassXport (30,302 views)
77. Software:Mayu (30,184 views)
78. Software:ProbID (29,260 views)
79. TPP 4.3.1: Installing on Ubuntu 10.04 (28,670 views)
80. TPP:Building Windows-native binaries with Mingw (28,634 views)
81. Developer: Boost CPP libraries (28,358 views)
82. Software:Out2XML (28,266 views)
83. TPP:4.6.0 Release Notes (28,016 views)
84. Software:Tandem2XML (27,009 views)
85. TPP:5.0.0 Release Notes (26,860 views)
86. Software:Mascot2XML (26,643 views)
87. Software:Prequips (26,085 views)
88. TPP:5.1.0 Release Notes (25,942 views)
89. Recipe for generating proteotypic peptides for example database (25,767 views)
90. Software:QualScore (25,361 views)
91. Software:JRAP (25,073 views)
92. GetTransitionsAPI (25,072 views)
93. Software:Petunia (25,053 views)
94. TPP:Installing on Ubuntu 7.04 (24,949 views)
95. Software:SBEAMS (24,312 views)
96. Software:SWATHProphet (24,281 views)
97. Software:SpecArray (24,125 views)
98. Glyco-peptide TODO list (23,822 views)
99. Software:Corra (23,175 views)
100. PABST (22,974 views)
101. Software:PeptideSieve:Build (22,903 views)
102. Processing glycopeptide data (22,799 views)
103. Software:PeptideAtlas (22,599 views)
104. Software:SubsetDB (21,908 views)
105. TPP AMZTPP:PetuniaTutorial (21,476 views)
106. TPP:6.0.0 Release Notes (21,285 views)
107. Using SBEAMS (20,165 views)
108. TPP:4.2.0 Release Notes (20,126 views)
109. Software:da2tpp (19,815 views)
110. Software:Cytoscape (19,485 views)
111. PeptideAtlas software (18,103 views)
112. Linux Installation Guides (17,997 views)
113. TPP 5.0.0: Installing on Ubuntu 16.04 (17,802 views)
114. TPP 4.2.1: Installing on Ubuntu 9.04 (17,502 views)
115. Formats:Overview (17,478 views)
116. TPP:4.6.1 Release Notes (17,386 views)
117. TPP:Building Windows-native binaries with Visual Studio 2005 (17,113 views)
118. ComputationalPredictionofProteotypicPeptides (17,060 views)
119. Debugging:Working with boost::shared ptr (16,518 views)
120. Software:MZIdentML (16,467 views)
121. Links on mindfulness, meditation, and Buddhism (16,318 views)
122. Glyco-peptide (16,213 views)
123. Spectrast create.params (15,999 views)
124. Software:MsXML2Other (15,777 views)
125. TPP:4.5.1 SVN Log (15,581 views)
126. Software:PepXMLViewer (15,528 views)
127. Software:Out2Summary (15,072 views)
128. TPP:5.2 Installation (14,687 views)
129. TPP 5.1.0: Installing on Ubuntu 16.04 LTS (14,523 views)
130. TPP:4.4.1 Release Notes (14,468 views)
131. Software:XLink (14,284 views)
132. AMZTPP:FAQ (13,902 views)
133. Software:SPE (13,470 views)
134. Software:pkl2mzXML (13,349 views)
135. Protein identification terminology (13,221 views)
136. Software:PeptideSieveRetrainingTurtorial (13,116 views)
137. TPP:4.1 Release Notes (13,105 views)
138. Formats:protXML (12,958 views)
139. TPP:Mascot and the TPP (12,828 views)
140. TPP:5.0 Installation (12,651 views)
141. Using mProphet at ISB (12,620 views)
142. Respect your Results (12,544 views)
143. TPP:5.1 Installation (12,443 views)
144. TPP:5.2.0 Release Notes (12,299 views)
145. Debugging:Understanding XSL-Generating Code in Perl (12,291 views)
146. TPP:Installing on Ubuntu 8.10 (12,023 views)
147. Software:StPeter (11,794 views)
148. FetchDataset (11,119 views)
149. Citing the TPP (11,083 views)
150. Mayu (10,962 views)
151. TPP:Sequest and the TPP (10,926 views)
152. Spectrast.usermods (10,843 views)
153. Prequips:FAQ (10,754 views)
154. Export questions discussion list (10,483 views)
155. TPP:Getting the sourcecode for a windows build (10,412 views)
156. TPP:4.5.0 SVN Log (10,199 views)
157. TPP Tutorials (9,857 views)
158. TPP:4.6.2 SVN Log (9,760 views)
159. Software:RAP (9,611 views)
160. Raw MS file conversion (9,376 views)
161. TPP:4.5.2 Release Notes (9,359 views)
162. GetProteinAPI (9,185 views)
163. TPP:4.2.1 Release Notes (8,457 views)
164. TPP TWA (8,407 views)
165. TPP:ProbID and the TPP (8,405 views)
166. TPP:Directory Layout (8,246 views)
167. Bash/tcsh syntax differences (8,207 views)
168. TPP:5.0.0 SVN Log (7,816 views)
169. TPP:4.8.0 SVN Log (7,777 views)
170. Tutorial:StPeter1 (7,648 views)
171. TPP:4.6.3 SVN Log (7,630 views)
172. TPP:4.7.0 SVN Log (7,377 views)
173. TPP:4.6.0 SVN Log (7,238 views)
174. MS level 2 (7,053 views)
175. TPP AMI 4.7.0 README (6,992 views)
176. TPP:V5Tasks (6,623 views)
177. TPP WISB Demo2012 (6,418 views)
178. TPP:Phenyx and the TPP (6,233 views)
179. TPP 5.x development: Installing on Ubuntu 16.04 (6,017 views)
180. Prequips:Bugs (5,682 views)
181. NewFrontPage (5,620 views)
182. Alt NxST search strategy (5,527 views)
183. TPP:4.7.1 SVN Log (5,500 views)
184. TPP:4.3.0 Release Notes (5,443 views)
185. Prequips:Wishlist (5,410 views)
186. GetProteinsAPI (5,214 views)
187. TPP:5.1.0 SVN Log (4,811 views)
188. SearchProteins (4,756 views)
189. TPPDev:ReleaseChecklist (4,543 views)
190. Software:DidIScanThat (4,540 views)
191. TPP:5.2.0 SVN Log (4,516 views)
192. Link (4,492 views)
193. TPP:4.5.2 SVN Log (4,451 views)
194. Installing and building TPP on Windows (4,335 views)
195. TPP testimonials (4,305 views)
196. TPPDev:Branching (4,027 views)
197. PeptideAtlas Pipeline Retool 2012/13 (3,916 views)
198. TPP AMI 4.6.3 README (3,880 views)
199. TPP 6.1.0: Installing on Ubuntu 20.04 LTS (3,825 views)
200. Software:PeptideSieve:Builld (3,820 views)
201. Scheduling on regis cluster (3,714 views)
202. Prequips:Documentation (3,506 views)
203. Custom digest site (3,443 views)
204. Spectra assignment (3,421 views)
205. Ms/ms (3,246 views)
206. TPP AMI 4.8.0 README (3,230 views)
207. TPP 6.0.0: Installing on Ubuntu 20.04 LTS (3,172 views)
208. TPP AMI 4.7.1 README (3,145 views)
209. My new page (3,051 views)
210. TPP AMI 4.6.2 README (2,974 views)
211. TPP:6.1.0 Release Notes (2,908 views)
212. NewGlycoPage (2,881 views)
213. TPP:4.6.1 SVN Log (2,750 views)
214. Software:TPP:EC2 (2,717 views)
215. Debugging:CGI programs (2,634 views)
216. TPP:Files and Formats (2,620 views)
217. Software:Tomcat (2,436 views)
218. TPP 6.2.0: Installing on Ubuntu 22.04 LTS (2,159 views)
219. TPP:6.3.0 Release Notes (2,074 views)
220. Running the TPP Singularity image (1,624 views)
221. TPP:6.2.0 Release Notes (1,458 views)
222. TPP:NovorIntegration (1,446 views)
223. TPP:7.0.0 Release Notes (747 views)
224. TPP 7.0.0: Installing on Ubuntu 22.04 LTS (144 views)

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