Proteome Discoverer 1.3 Information

Proteome Discoverer 1.3 new features includes:

*. phpsphoRS: PTM scoring
*. percolator : increase true positive PSM (peptide spectral match)
*. integrate proteinCenter: annotation
*. 64-bit windows support


Requirements:

Type	Requirements
Disc Space	2 GB
Memory	2 GB
Processor	1
CPU-Speed	1333 MHz
Display	1280x1024
Font DPI	96 dpi
OS Language	English
.Net 3.5 SP1	Present
.Net 4.0	Present

ref:

Proteome_Discoverer_1.3_Software_Enhanced_Tools_For_Protein_Identification
http://apps.thermoscientific.com/media/SID/LSMS/PDF/LSMSUsersMtg/Indianapolis/Proteome_Discoverer_1.3_Software_Enhanced_Tools_For_Protein_Identification.pdf

Recent_Developments_in_Thermo_Scientific_LSMS_Proteomics_Software
http://apps.thermoscientific.com/media/SID/LSMS/PDF/LSMSUsersMtg/Indianapolis/Recent_Developments_in_Thermo_Scientific_LSMS_Proteomics_Software.pdf


Install guide
http://sjsupport.thermofinnigan.com/TechPubs/manuals/Discoverer_Install.pdf

User Guide
http://sjsupport.thermofinnigan.com/TechPubs/manuals/Discoverer_User.pdf

Trans-Proteomic Pipeline (TPP) 4.5.0 release

http://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.0_Release_Notes

 New Features

• New iModelParser.cgi tpp; fpr viewing iProphet models.

• New PTMProphetParser tool.

• New RTCatalogParser tool for cataloging retention times.

• xinteract
  • New features, report collision energy, report compensation voltage

• InteractParser:
  • New features, report collision energy, report compensation voltage
  • Adding collision energy and compensation voltage for FAIMS as optional attributes in pepXML schema spectrum_query
  • SearchHit Changes, also defines bool_hash used in RTCatalog.
  • Read collision energies in all msms_run_summaries, not just the first one encountered per pepXML file.
  • Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.
  • New feature precursor intensity in pepXML
  • Option for recording the retention_time_sec in pepXML.

• Windows installer now allows you to choose which components (such as msconvert) to install. This was done to comply with the licensing requirements of Proteowizard/msconvert. The installer was also streamlined by removing some of the dialog/steps, improving the language of the instructions and changing when certain checks are done as part of the installation process.

• New Javascript-based spectrum viewer (Lorikeet)

• Petunia:
  • Added direct access to switch a directory in File Browser
  • Added user input to pass parameters directly to the command-line (certain executables at this time), including simple validation

[edit]

Improvements/Changes

• The older ProteoWizard based RAMP mzML/mzXML parse was replaced with mzParser to address some performance problems in a number of different programs.

• PepXMLViewer.cgi
  • Version added to index file so that old index files get regenerated instead of crashing the viewer
  • Index files now use longs for offsets to support large files
  • Added collision_energy, precursor_intensity and compensation_voltage support for Crux
  • Added PTMProphetParser support.

• RefreshParser
  • I->L conversion on peptide and proteins to map to all indistinguishable peptides in the proteins.

• ASAPRatio
  • New options added to quantify only above certain probability.

• PeptideProphetParser
  • tweak pI model to model only +-5 stdev from mean pI for run.
  • update to correct problem with latest version of Myrimatch which removed some scores in the reports.

• XPressPeptideParser
  • Allow for proper quantitation of combined files where modified masses might be off depending on search engine and use of average vs monoisotopic mass in the search.

• RAMP
  • Adding parsing of compensationVoltage (FAIMS).

• iProphet
  • Clear out tophit hashes before recomputing. Separate SearchHit in a different class.
  • Remove any peptideprophet or prior interprophet analysis_summary tags.

• New pepXML schema update for collision_energy and compensation_voltage

• Add scan counters to use as scan numbers when this info is not available in the mzML file (e.g. Agilent QTrap Data)

• Fix boost build to work with zlib125's directory structure, delete old zlib123-dll.tar.bz2

• Switch to zlib v1.2.5 and tweaks for MingW build

• Rules for fetching Proteowizard and copying msconvert in the Windows installer were added to the Makefile to make builds more automated.

• Petunia:
  • Make Tandem the default pipeline;
  • Added option to run Tandem2XML immediately after searching;
  • Added support for two missing enzymes in ->pepXML, as well as semi-enzyme support;
  • Added IPROPHET option to ProteinProphet
  • Adjusted Xpress defaults;
  • Centralized code that creates links to open files in respective viewers;
  • Moved "timeout" link to the right to avoid overlap with update page link;
  • Added confirmation message when switching pipeline type;
  • Shortened some menu titles to save space;
  • Added mouse-over tooltips for menu items and navigation tabs;
  • Added NIGMS logo and credits; replacing NHLBI's
  • Took out obsolete SpectraST user options; added decoy-related options and Append To Library feature
  • Minor formatting fix to PepC page
  • Small code formatting/alignment changes.
  • Updated meaning of $in_windows and introduced $in_cygwin vars;
  • Removed some seemingly unused code.

• Protein Sequence Viewer:
  • Added html comments for easier scrubbing of page (by exporTPP.pl)

• Peptide-Protein Weights Viewer:
  • Fixed page format to fit page width, got rid of wasted space;
  • Minor HTML tweaks;
  • Added svn rev;
  • Code clean-up: took out unused code, re-tabbed/formatted.

[edit]

Bug fixes

• PepXMLViewer
  • Fixed crash when empty filtered set is returned.
  • Fixed problem when using commandline generated index which didn't print the queryString so we fake one.

• Tandem2XML
  • Filter out extension from Tandem spectrum names.

• iModelParser.cgi
  • Fix bugs with getting page to display. Now displays but the overlapping colors of gnuplot don't work. For best results use gnuplot 4.4.

• InteractParser
  • Fix Q[111] and E[111] modification reporting in pepXML for OMSSA, max rank option to not report hits above a certain hit_rank.

• iProphet
  • When the pepXML already contains the iProphet tags filter them out, including the end tag.
  • Correct the outputting of extra </spectrum_query> tags.
  • Changes to pepXML writer to correct extra tag issue when iProphet is run on pepXML that already contains iProphet tags.

• Fix parsing of Phenyx search results.

• Petunia:
  • Minor bug fix when file is not present (as opposed to unreadable).
  • Fixed broken Set Working Dir feature, also fixed link when output is a directory;
  • Fixed bug that FileChooser to fail when pressing 'Enter' to switch directory

[edit]

Miscellaneous

• Nothing to report

[edit]

Known Issues

• There is an issue with using the 64bit version of ActiveState's Perl. While the installer recognizes that it is installed all of the Perl programs and scripts are hard-coded to use C:\perl\bin\perl -- the default location for 32bit installations of ActiveState perl. You can either install the 32bit version, or modify all of the scripts to use the 64 bit location (C:\perl64\bin\perl).

[edit]

Getting the TPP Software

• Download the TPP version 4.5.0 native windows installer (TPP_Setup_v4_5_RAPTURE_rev_1.exe) from the Sashimi SourceForge project file release page:

"http://sourceforge.net/projects/sashimi/files/"

MS File Reader 2.2 now support x64 Windows !

MS File Reader finally support Windows x64.

Now you can use software that need MS File Reader, like MaxQuant, in Windows x64 with it.

Just downlaod the latest MS File Reader http://sjsupport.thermofinnigan.com/public/detail.asp?id=703 and install it.

Using ReAdW to convert Thermo .RAW files to mzXML

To run ReAdW, you need to install Xcalibur first.

1. download program:

ReAdW program download:

http://sourceforge.net/projects/sashimi/files/ReAdW%20%28Xcalibur%20converter%29/ReAdW-4.3.1/ReAdW-4.3.1.zip/download

zlib1donwload

https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-0/win_lib/zlib123-dll/zlib1.dll

2. put the readw.exe and zlib1.dll in the same directory.

3. input something like below by command line:

ReAdW -v --mzXML test.raw

 

Reference:

http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW