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- TPP:Example data analysis (2562 bytes)
9: == Example Data Analysis ==
11: ==== Sequest Searched Data Example ====
12: ===== Getting Example Data =====
14: ...wing link: http://tools.proteomecenter.org/sample_data/raftapr_searched.tgz
15: ## Save the file in the <b>c:\Inetpub\wwwroot\ISB\data</b> directory on your computer - Processing glycopeptide data (6720 bytes)
5: # Create a target database where the N of all glyco sites is swapped for...
6: # Search glyco data against this DB, allowing an optional modificatio...
10: ...rams are the same as usual except that the target database is ipi.HUMAN.v3.38_forwdecoy_nxst.fasta:
41: # create search database with NxS/T changed to NBS/T. This will
42: # make nxst and 'reverse' versions of the source database, called
Page text matches
- Main Page (6427 bytes)
12: ...sions range from installation support to advanced data processing questions and feature requests. Pleas...
14: ==[[Formats:Overview|SPC open proteomics data formats]]: mzXML, pepXML, protXML==
22: * conversion of raw data to open formats;
23: ...y searching with [[SpectraST]], and cross-linking data with [http://www.kojak-ms.org/ Kojak];
34: ... where simple operations can be performed on this data and messages can be passed to other more sophisti... - TPP:V5Feedback (11460 bytes)
22: ...ave install over TPP 4.8, it sets the default tpp data directory to the old directory under Inetpub. Bu...
23: ...old ISB directory, if that isn't there then {app}/data.''
64: * <s>comet-fastadb.cgi crashes if database doesn't exist (or for that matter if no cgi o...
77: ...eration not permitted command "gnuplot.exe c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.00417.0041...
78: ...11.splib&LibFileOffset=413954123&QueryFile=c:/TPP/data/spectrast/OR20080317_S_SILAC-LH_1-1_01.mzML&Query... - Software:Prequips (1386 bytes)
3: ...tegration, visualization and analysis of LC-MS/MS data.
5: ...icroarray data or sequence information. Currently data can be read from mzXML, pepXML, Bioworks (tabular...
7: ...teractive and linked to each other, making visual data exploration straightforward.
9: ...n of large heterogeneous data sets without manual data conversion. - Prequips:FAQ (1189 bytes)
25: # Select '''Raw Data Analysis''' as analysis type. - Software:Prequips:Inclusion List Builder (3897 bytes)
28: === Sample Data ===
30: Download the ZIP archive below for a sample data set to explore the features of the Inclusion List...
32: ...download/data/prequips_ilb_sample-data.zip Sample Data] (80 MB). Contains 1 mzXML file in centroid mode ... - TPP:Developer Documentation (23931 bytes)
46: Webserver with access to data directories. See configuration section below. ...
50: ...an "xsl transform" processor for manipulating XML data.
124: Ideally, all data directories should be cross mounted under the web...
199: ====Conversion of raw spectroscopy data to mzXML format====
211: *For Mascot results, you must specify the database used for search: - Software:Overview (3074 bytes)
16: ==Data Conversion==
29: ...rn]]: software for quantitative analysis of LC-MS data by a combined MS1 and MS2 approach
35: ...ophet]]: A tool for statistical analysis of SWATH data and discovery of modifications
42: ...ools for analysis and visualization of biological data
54: ...DB|SubsetDB]]: tools for handling FASTA formatted databases - TPP:Files and Formats (299 bytes)
3: ;mzXML: interchange of MS/MS-level data; ISB-developed
4: ;pepXML: interchange of peptide-level data; ISB-developed
5: ;protXML: interchange of protein-level data; ISB-developed - TPP:Windows Cygwin Installation (7499 bytes)
93: ===[[TPP:Example data analysis|Example Data Analysis]]=== - Software:SBEAMS (2104 bytes)
7: ...composed of a unified state-of-the-art relational database management system (RDBMS) back end, a collect...
11: ...at other sites with a little persistence and Perl/Database expertise. If you make improvements to the co... - TPP:Frequently Asked Questions (5647 bytes)
24: ===How do I interact with data from TPP?===
25: Data is generally expected to be viewed from within a ...
43: *Use CLEVEL when the data is misbehaving and PeptideProphet model is under-...
74: ...peline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite''; - TPP:7.0.0 Release Notes (6884 bytes)
21: ... shuffling and outputting the last protein in the database and outputting the penultimate twice...proble...
27: ...e is not parsed a second time and simply uses the data that was parsed in the readHeader() function call...
28: ...th the spectrum and having an actual ion mobility data array.
35: ...unts to prevent overclassification due to lack of data.
40: ...sity peaks which can occur rarely on some timsTOF data and causes PTMProphet to fail. - Software:PeptideProphet (1728 bytes)
8: ...data by eliminating the need to manually validate database search results. In addition, it can facilitat...
11: ...racy of peptide identifications made by MS/MS and database search." Anal Chem 74:5383-92. [http://tools.... - Software:ProteinProphet (6941 bytes)
5: ...lities for protein identifications based on MS/MS data. ProteinProphet makes use of results from Pepti...
21: ... (ASAP must have been run previously on interact dataset)
30: ...ly on all input interact datasets with mz/XML raw data format)
44: ==Caution for large datasets==
46: ...ds to overestimate probabilities when given large datasets (more than, say, 500,000 spectra). Here is wh... - Software:ASAPRatio (1791 bytes)
9: ...ing confidence intervals from ICAT-type ESI-LC/MS data. The software first uses a Savitzky- Golay smooth...
12: ...istical analysis of protein abundance ratios from data generated by stable isotope dilution and tandem m... - Software:Pep3D (1087 bytes)
8: ...entification. The results can be used to evaluate data quality among its many applications.
11: ...rsold R. (2004) "A tool to visualize and evaluate data obtained by liquid chromatography / electrospray ... - Software:TPP (8918 bytes)
103: RAMP: mzXML data parser
110: ===Database Search Tools===
117: ==Example Data Analysis==
118: *[[TPP:Example data analysis|Example Data Analysis]]
136: ...e, daily discussions ranging from installation to data processing. All users, new and experienced, enco... - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
18: ...de>/data</code>. If you want to make your default data location elsewhere, change accordingly
47: ...usr/local/tpp and make the default data location /data. You may wish to install in a different location,...
51: sudo mkdir /data
52: sudo chown tpp.tpp /data
70: ... match the locations you created above. Leave TPP_DATAURL and TPP_BASEURL as is unless you're putting th... - Software:SpecArray (1001 bytes)
6: ...e vs. sample expression array from a set of LC-MS data, obtained by analyzing peptide samples under iden...
8: * Pep3D: Generate 2D gel type images from LC-MS data (''Note: Pep3D is also integrated into the [[Soft...
9: * mzxml2dat: Denoise and centroidize LC-MS data in mzXML file format and convert them into binary...
10: ...st: Extract a list of peptide features from LC-MS data - Software:mzStar (1909 bytes)
9: ...mzStar. This has resulted in major data loss for data that was centroided with this converter. Current...
14: SCIEX/ABI Analyst (.WIFF) format MS/MS data to [[Formats:mzXML|mzXML]] converter. '''(RETIRE...
17: Visual Basic application to convert data from a SCIEX/ABI Q-STAR instrument into [[Formats...
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