forked from crux-toolkit/crux-toolkit.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
399 lines (355 loc) · 14 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
<!DOCTYPE html>
<html>
<head>
<title>Crux tandem mass spectrometry analysis software</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="stylesheet" type="text/css" href="styles.css">
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-26136956-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
<script type="text/javascript">
// Main Menu
$( document ).ready(function() {
var pull = $('.btn');
menu = $('nav ul');
menuHeight = menu.height();
$(pull).on('click', function(e) {
e.preventDefault();
menu.slideToggle();
});
$(window).resize(function(){
var w = $(window).width();
if(w > 320 && menu.is(':hidden')) {
menu.removeAttr('style');
}
});
});
</script>
<!--(index.html only) Start JS function for dynamically resizing the image map that links elements on schematic.png-->
<script type="text/javascript">
window.onload = function () {
var ImageMap = function (map, img) {
var n,
areas = map.getElementsByTagName('area'),
len = areas.length,
coords = [],
previousWidth = 1125; // width of original schematic.png
for (n = 0; n < len; n++) {
coords[n] = areas[n].coords.split(',');
}
this.resize = function () {
var n, m, clen,
x = img.offsetWidth / previousWidth;
for (n = 0; n < len; n++) {
clen = coords[n].length;
for (m = 0; m < clen; m++) {
coords[n][m] *= x;
}
areas[n].coords = coords[n].join(',');
}
previousWidth = img.width;
return true;
};
window.onresize = this.resize;
}
imageMap = new ImageMap(document.getElementById('schematic_map'), document.getElementById('schematic_image'));
imageMap.resize();
}
</script>
<!--(index.html only) End JS -->
</head>
<body>
<div class="page-wrap">
<nav>
<div class="btn">
</div>
<img src="images/crux-logo.png" id="logo"></a>
<ul id="navitems">
<li><a href="index.html">Home</a></li>
<li><a href="download.html">Download</a></li>
<li><a href="fileformats.html">File Formats</a></li>
<li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
</ul>
</nav>
<div id="content">
<!-- START CONTENT -->
<div id="schematic">
<img id="schematic_image" src="images/schematic.png" usemap="#commands-files" border="0" width="100%" alt="" />
<map name="commands-files" id="schematic_map">
<area shape="rect" coords="253,135,349,169" alt="tide-index" href="commands/tide-index.html">
<area shape="rect" coords="260,247,342,278" alt="bullseye" href="commands/bullseye.html">
<area shape="rect" coords="510,100,612,132" alt="tide-search" href="commands/tide-search.html">
<area shape="rect" coords="528,191,595,222" alt="comet" href="commands/comet.html">
<area shape="rect" coords="512,281,613,335" alt="search-for-xlinks" href="commands/search-for-xlinks.html">
<area shape="rect" coords="776,100,873,132" alt="percolator" href="commands/percolator.html">
<area shape="rect" coords="791,160,861,192" alt="barista" href="commands/barista.html">
<area shape="rect" coords="783,222,866,252" alt="q-ranker" href="commands/q-ranker.html">
<area shape="rect" coords="784,281,867,334" alt="spectral-counts" href="commands/spectral-counts.html">
</map>
<img src="images/crux-logo.png" style="width:200px; float:left; padding:10px;">
<p>The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. The toolkit includes several search engines for both standard and cross-linked database search, as well as a variety of pre- and post-processing engines for assigning high-resolution precursor masses to spectra, assigning statistical confidence estimates to spectra, peptides and proteins, and performing label free quantification. Crux comes pre-complied for the Linux, Windows and MacOS operating systems. It is implemented as a single program that offers a wide variety of commands. If you use Crux in your research, please cite:
<br />
<span class="indentcitation">Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael
J. MacCoss and William Stafford
Noble. <a href="http://noble.gs.washington.edu/papers/park2008rapid.html">"Rapid
and accurate peptide identification from tandem mass spectra."</a>
<i>Journal of Proteome Research.</i> 7(7):3022-3027, 2008.</li></span>
<br /><br />
For a more up-to-date description of Crux, please read:<br />
<span class="indentcitation">Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas,
Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry
Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael
J. MacCoss and William Stafford
Noble. <a href="http://pubs.acs.org/doi/abs/10.1021/pr500741y">"Crux:
rapid open source protein tandem mass spectrometry
analysis."</a> <i>Journal of Proteome Research.</i>
13(10):4488-4491, 2014.</span>
</p>
</div>
<br />
<p/>
Crux is provided as a single executable that supports the following
commands:</p>
<table id="commandstable">
<tr>
<td colspan="2"><b>Primary commands</b></td>
</tr>
<tr>
<td><a href="commands/bullseye.html">bullseye</a></td>
<td>Assign high resolution precursor m/z values to MS/MS data using the Hardklör algorithm.
</tr>
<tr>
<td>
<a href="commands/tide-index.html">tide-index</a></td>
<td>
Create an index of all peptides in a fasta file, for use in subsequent
calls to <code>tide-search</code>.</td>
</tr>
<tr>
<td>
<a href="commands/tide-search.html">tide-search</a></td>
<td>
Search a collection of spectra against a sequence database, provided
either as a FASTA file or an index, returning a collection of
peptide-spectrum matches (PSMs). This is a fast search engine, but it
runs most quickly if provided with a peptide index built
with <code>tide-index</code>.</td>
</tr>
<tr>
<td>
<a href="commands/cascade-search.html">cascade-search</a></td>
<td>
An iterative procedure for incorporating information about peptide
groups into the database search and confidence estimation
procedure.</td></tr>
<tr>
<td>
<a href="commands/comet.html">comet</a></td>
<td>
Search a collection of spectra against a sequence database, returning
a collection of PSMs. This search engine runs directly on a protein
database in FASTA format.</td>
</tr>
<tr>
<td>
<a href="commands/percolator.html">percolator</a></td>
<td>
Re-rank and assign confidence estimates to a collection of PSMs using
the Percolator algorithm. Optionally, also produce protein rankings
using the Fido algorithm.</td></tr>
<tr>
<td>
<a href="commands/q-ranker.html">q-ranker</a></td>
<td>
Re-rank a collection of PSMs using the Q-ranker algorithm.</td></tr>
<tr>
<td>
<a href="commands/barista.html">barista</a></td>
<td>
Rank PSMs, peptides and proteins, assigning a confidence measure to each
identification.</td></tr>
<tr>
<td>
<a href="commands/search-for-xlinks.html">search-for-xlinks</a></td>
<td>
Search a collection of spectra against a sequence database, finding
cross-linked peptide matches.</td></tr>
<tr>
<td>
<a href="commands/spectral-counts.html">spectral-counts</a></td>
<td>
Quantify peptides or proteins using one of three spectral counting
methods.</td></tr>
<tr>
<td>
<a href="commands/pipeline.html">pipeline</a></td>
<td>
Given one or more sets of tandem mass spectra as well as a protein
database, this command runs a series of Crux tools and reports all of
the results in a single output directory.
</td></tr>
<tr>
<td colspan="2"><b>Utilities</b></td>
</tr>
<tr>
<td>
<a href="commands/assign-confidence.html">assign-confidence</a></td>
<td>
Assign statistical confidence measures to each PSM in a given set.</td></tr>
<tr>
<td>
<a href="commands/generate-peptides.html">generate-peptides</a></td>
<td>
Extract from a given set of protein sequences a list of target and
decoy peptides fitting the specified criteria.</td>
</tr>
<tr>
<td>
<a href="commands/get-ms2-spectrum.html">get-ms2-spectrum</a></td>
<td>
Extract one or more fragmentation spectra, specified by scan number, from
an <code>MS2</code> file.</td>
</tr>
<tr>
<td><a href="commands/hardklor.html">hardklör</a></td>
<td>Identify isotopic distributions from high-resolution mass spectra.</td>
</tr>
<tr>
<td><a href="commands/make-pin.html">make-pin</a></td>
<td>Given a set of search results files, generate a pin file for input to
<code>crux percolator</code></td>
</tr>
<tr>
<td><a href="commands/param-medic.html">param-medic</a></td>
<td>Examine the spectra in a file to estimate the best precursor
and fragment error tolerances for database search.</td>
</tr>
<tr>
<td>
<a href="commands/predict-peptide-ions.html">predict-peptide-ions</a></td>
<td>
Given a peptide and a charge state, predict the m/z values of the
resulting fragment ions.</td>
</tr>
<tr>
<td>
<a href="commands/print-processed-spectra.html">print-processed-spectra</a></td>
<td>
Process spectra as for scoring xcorr and print the results to a file.</td></tr>
<tr>
<td>
<a href="commands/psm-convert.html">psm-convert</a></td>
<td>
Convert a file containing peptide-spectrum matches (PSMs) from one
format to another.</td></tr>
<tr>
<td>
<a href="commands/subtract-index.html">subtract-index</a></td>
<td>Subtract one index file from another, assuming both were generated
by tide-index.</td></tr>
<tr>
<td>
<a href="commands/xlink-assign-ions.html">xlink-assign-ions</a></td>
<td>Given a spectrum and a pair of cross-linked peptides, assign theoretical
ion type labels to peaks in the observed spectrum.</td>
</tr>
<tr>
<td>
<a href="commands/xlink-score-spectrum.html">xlink-score-spectrum</a></td>
<td>Takes a defined cross-linked peptide, a spectra file, and a scan number,
and will calculate the XCorr score a number of different ways.</td>
</tr>
<tr>
<td>
<a href="commands/localize-modification.html">localize-modification</a></td>
<td>Finds, for each peptide-spectrum match (PSM) in a given set, the most
most likely location along the peptide for a post-translational
modification (PTM). The mass of the PTM is inferred from the difference
between the spectrum neutral mass and the peptide mass.</td>
</tr>
<tr>
<td>
version</td>
<td>
Print the Crux version number to standard output, then exit.</td>
</tr>
<tr>
<td colspan="2"><b>Utilities for processing tab-delimited text files</b>
</tr>
<tr>
<td>
<a href="commands/extract-columns.html">extract-columns</a></td>
<td>Print specified columns from a tab-delimited file.</td>
</tr>
<tr>
<td>
<a href="commands/extract-rows.html">extract-rows</a></td>
<td>Print specified rows from a tab-delimited file.</td>
</tr>
<tr>
<td>
<a href="commands/stat-column.html">stat-column</a></td>
<td>Collect summary statistics from a column in a tab-delimited file.</td>
</tr>
<tr>
<td>
<a href="commands/sort-by-column.html">sort-by-column</a></td>
<td>Sort a tab-delimited file by a column.</td>
</tr>
</table>
<!-- END CONTENT -->
</div>
</div>
<footer class="site-footer">
<div id="centerfooter">
<div class="footerimportantlinks">
<img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
<ul>
<li><a href="faq.html">Crux FAQ</a></li>
<li><a href="glossary.html">Glossary of terminology</a></li>
<li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
<li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
<li><a href="release-notes.html">Release Notes</a></li>
<li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
<li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
<li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
</ul>
</div>
<div class="footerimportantlinks tutoriallinks">
<img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
<ul>
<li><a href="tutorials/install.html">Installation</a></li>
<li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
<li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
<li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
<li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
</ul>
</div>
<div id="footertext">
<p>
The original version of Crux was written by Chris Park and Aaron Klammer
under the supervision
of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
MacCoss</a>
and <a href="http://noble.gs.washington.edu/~noble">Prof. William
Stafford Noble</a> in the Department of Genome Sciences at the
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
<br />The complete list of contributors
can be found <a href="contributors.html">here</a>.
<br />
<br />
Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
</p>
</div>
</div>
</footer>
</body>
</html>