diff --git a/xtandempipeline/doc/xtandem_pipeline.pdf b/xtandempipeline/doc/xtandem_pipeline.pdf index 01ffce294d3c1a6ebbd42e25f5fcb64969429fd6..5fe8402641dc99367a9826cd7c475777e0fce623 100644 Binary files a/xtandempipeline/doc/xtandem_pipeline.pdf and b/xtandempipeline/doc/xtandem_pipeline.pdf differ diff --git a/xtandempipeline/doc/xtandem_pipeline.tex b/xtandempipeline/doc/xtandem_pipeline.tex index 45c83aed9e93c1ab586ee2416c45834c2fc1d25d..1547a56b9a724920201311d6dda2fee64217d636 100644 --- a/xtandempipeline/doc/xtandem_pipeline.tex +++ b/xtandempipeline/doc/xtandem_pipeline.tex @@ -20,7 +20,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\ \includegraphics[width=1cm]{images/pappso.pdf} } \title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results} -\date{10 May 2011} +\date{15 February 2012} %Modification des entetes et pied de page + marges \geometry{top=3cm, bottom=3cm, left=2cm, right=2cm} @@ -419,5 +419,35 @@ In this case, the column corresponding to the normal and reverse search are indi \label{fdr2} \end{figure} +\pagebreak + +\section{Changelog} +\subsection{"Tubuline" versions} +\begin{description} + \item[3.2.0] Identification from Mascot dat file can now be imported and filtered. All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\\ + Correction of FDR calculation from Reverse/Decoy search. +\end{description} + +\subsection{"Kératines" versions} +\begin{description} + \item[3.1.5] Add support of phosphorylation neutral loss and enhanced ETD detection on MS2 spectra.\\ + Correction of MassChroQ export. + \item[3.1.4] Add support for viewving ETD spectra after automatic detection. + \item[3.1.3] Corrected bug of xtandem preset. Refine analysis was never start instead refine param is set to yes.\\ + Adds a new annotated spectrum renderer and bug fix on ODS export. + \item[3.1.2] Add export results on Open Document Spreadsheet (.ods) file.\\ + Correction of bugs (Grouping, PepNovo export, ...). + \item[3.1.1] FDR computation are now compatible with reverse option of X!Tandem. + \item[3.1.0] Algorithm of grouping have been completly rewritten : + \begin{itemize} + \item Older project must be refiltered to be properly grouped. + \item Phosphopeptide filtering have been enhanced to correspond to : + \begin{itemize} + \item SubGroup represents the number of phosphosites + \item Group represents the number of phosphoproteins + \end{itemize} + \item Configuration file have been modified and must be parameter again +\end{itemize} +\end{description} \end{document} diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java index b26f40dbb60c81848bdcda772e97a87d43568aa5..94c8b4502e4f4bf005cfaf8368185281900d07e9 100644 --- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java +++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java @@ -41,8 +41,8 @@ public class XtandemPipelineMain { * @return * @return */ - static public String version = "3.1.5"; - static public String versionName = "Kératine Moustachue"; + static public String version = "3.2.0"; + static public String versionName = "Tubuline squeletique"; public static String about = "X!Tandem Pipeline is developped by PAPPSO team (http://pappso.inra.fr) by Benoit Valot and Olivier langella.\n\n" + "This software is distributed under the terms of the GNU General Public License.\n\n" @@ -53,20 +53,9 @@ public class XtandemPipelineMain { + "If a protein is identified by two peptides with an evalue of O.O1, the protein evalue is O.OOO1.\n\n" + "So, we preconise to put -4 for the protein evalue filter instead of -8."; - public static String news = "3.1.5 : Add support of phosphorylation neutral loss and enhanced ETD detection on MS2 spectra.\n" - + "Correction of MassChroQ export.\n\n" - + "3.1.4 : Add support for viewving ETD spectra after automatic detection.\n\n" - + "3.1.3 : Corrected bug of xtandem preset. Refine analysis was never start instead refine param is set to yes\n" - + "Adds a new annotated spectrum renderer and bug fix on ODS export\n\n" - + "3.1.2 : Add export results on Open Document Spreadsheet (.ods) file.\n" - + "Correction of bugs (Grouping, PepNovo export, ...).\n\n" - + "3.1.1 : FDR computation are now compatible with reverse option of X!Tandem.\n\n" - + "3.1.0 : Algorithm of grouping have been completly rewritten : \n" - + "Older project must be refiltered to be properly grouped.\n\n" - + "Phosphopeptide filtering have been enhanced to correspond to :\n" - + "- SubGroup represents the number of phosphosites\n" - + "- Group represents the number of phosphoproteins\n\n" - + "Configuration file have been modified and must be parameter again"; + public static String news = "3.2.0 : Identification from Mascot dat file can now be imported and filtered."+ + " All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\n\n"+ + "Correction of FDR calculation from Reverse/Decoy search."; public static void main(String[] args) {