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- Software:Prequips:Inclusion List Builder (3897 bytes)
1: ...sion is a plug-in for [[Prequips]]. The Inclusion List Builder facilitates a directed LC-MS/MS that deco...
3: ...sion List Builders supports creation of inclusion lists and subsequent mapping of identified peptides to...
5: ...rg] if you experience problems with the Inclusion List Builder or Prequips.
10: [[Image:Ilb_concept.png|alt Inclusion List Builder concept]]
23: We currently provide the Inclusion List Builder only bundled with [[Prequips]]. - Export questions discussion list (2232 bytes)
1: ...ng open questions on the content or format of the list. (Back to main [[Glyco-peptide]] project page)
35: ...uld we have a final column with a comma-separated list of samples?
37: ...we use a consistent PeptideProphet cutoff for our lists? Peptide Atlas builds use 0.9 by default, which... - Glyco-peptide TODO list (1117 bytes)
28: * Send list to Bernd [done]
35: * Generate surface protein list [done]
36: * Merge lists
37: * Filter master list
40: * Generate theoretical list from cancer biomarker candidates [done]
Page text matches
- Main Page (6445 bytes)
36: ... can also serve as a data management tool, saving lists with user specified metadata (i.e., description ...
44: ...les, and other data in order to select transition lists according to user-defined priorities; - Prequips:Eclipse Setup (5641 bytes)
33: A list of projects will show up in the view. Select the ... - Prequips:FAQ (1189 bytes)
17: ...elect a project or a multi-sample analysis in the list on the right. ''Select '''Add directly to project...
29: # Select a single-sample analysis in the list on the right. - Software:Prequips:Inclusion List Builder (3897 bytes)
1: ...sion is a plug-in for [[Prequips]]. The Inclusion List Builder facilitates a directed LC-MS/MS that deco...
3: ...sion List Builders supports creation of inclusion lists and subsequent mapping of identified peptides to...
5: ...rg] if you experience problems with the Inclusion List Builder or Prequips.
10: [[Image:Ilb_concept.png|alt Inclusion List Builder concept]]
23: We currently provide the Inclusion List Builder only bundled with [[Prequips]]. - TPP:Developer Documentation (23931 bytes)
357: ;NOOCCAM: non-conservative maximum protein list
431: ...inProphet analysis to derive the simplest protein list to explain observed peptides
499: ...e occam's razor for degenerate peps (get max prot list, including many false positives) - TPP:Frequently Asked Questions (5647 bytes)
59: ...ghly''' encouraged to subscribe to the low-volume list spctools-announce, at http://groups.google.com/gr... - Software:ProteinProphet (6941 bytes)
8: ...level. We developed a model that has as input the list of peptides assigned to MS/MS spectra and corresp...
14: ... NOOCCAM: non-conservative maximum protein list
52: ...lly; rather, it allows us to present the shortest list of proteins needed to explain the data. - Software:XPRESS (1756 bytes)
8: ...xpression values are then updated in the INTERACT list. For those SEQUEST users interested in using the ... - Software:ASAPRatio (1791 bytes)
9: ...weighed samples. The software quickly generates a list of interesting proteins based on their relative a... - Software:TPP (8915 bytes)
35: * Subscribing to the low-volume mailing list [http://groups.google.com/group/spctools-announce... - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
245: - You should see a list of UPS and yeast proteins detected. Click around ... - Software:SpecArray (1001 bytes)
10: * PepList: Extract a list of peptide features from LC-MS data - Formats:pepXML (2274 bytes)
14: **Expands list of possible aa- and term- modification symbols
18: **Adds Calibr and Novor to engineType list
50: ...a should be submitted to the spctools-dev mailing list. - TPP:Installing on Ubuntu 7.04 (9446 bytes)
21: ...ral packages that you need to have installed. The list is provided
201: ## Ports to listen on for TPP
202: Listen 80
206: ## Ports to listen on for CPAS
207: #Listen 8080 - Software:Mascot2XML (2806 bytes)
66: ... if you wish to add an enzyme missing from the list. - TPP:X!Tandem and the TPP (5454 bytes)
42: ...s still known to function and their effects. This list represents the '''Advanced X! Series API''', and ... - Software:SpectraST (70083 bytes)
21: ...tra considered in sequence searching are very simplistic (e.g., only including b- and y-type ions, at a ...
43: * MRM transition list generation
67: * File list feature
78: * Detecting homologs in hit list
97: <code>spectrast <options> <list of files of appropriate formats></code> - Spectrast.params (3605 bytes)
13: # Selected List File Name - specify a file containing spectrum qu...
14: filterSelectedListFileName =
48: hitListTopHitFvalThreshold = 0.0
51: hitListLowerHitsFvalThreshold = 0.45
54: hitListShowHomologs = true - Spectrast create.params (4398 bytes)
25: # Use protein list to filter library
26: useProteinList = - TPP Tutorial v1 (43187 bytes)
54: dir lists the files in a directory
74: lists all the .html files in the directory that start ...
80: Lists all the files that start with ‘raft4041.’. ...
229: ...r search you will see the modifications below the list of amino acids in the matched peptide.
316: ...s are the same for each peptide assignment in the list. This is because the graphs reflect the PeptideP...
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