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- TPP:V5Feedback (11460 bytes)
46: ...iveInputFilename(char *inbuf, int inbuflen, char *spectrumName)</s>
49: * <s>Clicking on the ions2 link to view the spectrum in comet results in the pepxmlviewer results in a...
76: * <s>Clicking on spectrum id in the pepxmlviewer when viewing results of a ...
92: ...ctrast results</s>. Displayed when selecting the spectrum inthe pepxmlviewer on spectrast results.
94: ...-1_01.00417.00417.2.png) Seen when clicking on a spectrum in the pepxmlviewer on spectrast results.</s> - Software:Prequips (1386 bytes)
7: ...Prequips includes tabular data viewers as well as spectrum and chromatogram plots. It also provides an overv... - MS level 2 (326 bytes)
1: ...ation for [[spectra assignment]], either [[manual spectrum assignment|manually]] or automatically with a [[s... - Spectra assignment (180 bytes)
1: ...e to the precursor ion, based on the peaks in the spectrum. - Prequips:Bugs (772 bytes)
6: *Under Motif and GTK graphical viewers like spectrum plot and peak map are lacking axes and other info... - TPP:Developer Documentation (23931 bytes)
262: ;-M : MALDI mode: do not include spectrum spot number in mzXML file name
283: ...ines all analysis_summary elements, and reindexes spectrum_query elements. Makes a system call to pepxml2ht... - Debugging:Understanding XSL-Generating Code in Perl (1339 bytes)
7: ...dx={$xpress_index}&Timestamp={$asap_time}&Spectrum={$xpress_spec}&ratioType=' . <br /> - TPP:7.0.0 Release Notes (6884 bytes)
27: ...Peaks() is called after readHeader() for the same spectrum, the file is not parsed a second time and simply ...
28: ...etween having an ion mobility associated with the spectrum and having an actual ion mobility data array.
95: === [plot-msms-js.cgi (a.k.a. Lorikeet Spectrum Viewer):] ===
96: * add Seq2MS Generative Peptide Fragment Spectrum AI
100: * Lorikeet determine width and height for spectrum page based on whether the display is a phone or d... - Software:PeptideProphet (1728 bytes)
8: ... computes for each peptide assignment to an MS/MS spectrum a probability of being correct. We show that usin... - Software:ASAPRatio (1791 bytes)
1: [[Image:ASAPRatio_GUI.jpg|right]]
9: ...es are averaged and weighted by the corresponding spectrum intensity to obtain the peptide light:heavy ratio... - Software:Pep3D (1087 bytes)
8: ... plot; each spot is then a hyperlink to the ms/ms spectrum and identification. The results can be used to ev...
17: [[image:pep3d.jpg]] - Software:XLink (3210 bytes)
1: [[Image:XLink Viewer.jpg|thumb|right]]
11: ...ly, modified peptides should exist within a given spectrum as a doublet - a pair of peaks separated by the m... - TPP:X!Tandem and the TPP (5454 bytes)
7: ...r significant intensity manipulation of the query spectrum as described in the manuscript. You can access t...
11: <note label="spectrum, use conditioning" type="input">no</note>
66: GROUP, spectrum
71: 5. use conditioning - Modify spectrum using X!Tandem's internal rules prior to analysis... - Software:SpectraST (70083 bytes)
9: ...sitive identification is made if the experimental spectrum is sufficiently similar to one of the theoretical...
11: ...and identified peptide MS/MS spectra. The unknown spectrum can then by identified by comparing it to all the...
17: ...rch engine, needs about 5 to 20 seconds per query spectrum (against a human IPI database).
33: * Semi-empirical spectrum generation for amino acid substitutions ''(Contri...
42: * Decoy spectrum generation - Spectrast.params (3605 bytes)
13: ...lected List File Name - specify a file containing spectrum query names to be searched - Spectrast create.params (4398 bytes)
102: # Set the minimum number of peaks for a spectrum to be included
105: # Set the minimum SEQUEST deltaCn value for a spectrum to be included - TPP Tutorial v1 (43187 bytes)
19: [[image:Pipeline_Tutorial.jpg]]
207: ...MS data, view the complete SEQUEST output for any spectrum, look at the spectra with the matching ions highl...
212: [[Image:sequest_params.jpg]]
220: ...gnment.''' This does not give you an actual mass spectrum, but instead a new window containing the SEQUEST ...
222: [[Image:spectrum.png]] - Software:ProbID (2453 bytes)
25: ProbID may be run in single-spectrum or batch processing modes. ''Both options requir...
27: ===single MS/MS spectrum processing=== - Software:RAMP (2074 bytes)
14: *MS/MS spectrum viewer - RAMP - Software:JRAP (838 bytes)
8: guidelines on how to run the graphical spectrum viewer or you can just unpack
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