http://biodev.extra.cea.fr/docs/proline/ 2026-05-06T04:32:34+0200 http://biodev.extra.cea.fr/docs/proline/ http://biodev.extra.cea.fr/docs/proline/lib/tpl/dokuwiki/images/favicon.ico text/html 2016-07-07T14:20:48+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:decoysearches&rev=1467894048&do=diff Decoy Searches Proline handles decoy searches performed from two different strategies: * Concatenated searches: * A protein databank is created by concatenating target protein sequence to decoy protein sequence. Decoy could be created using reverse or random strategy. From Mascot or OMSSA point of view, a unique search is done using that databank. text/html 2013-11-27T15:41:45+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:fdrestimator&rev=1385563305&do=diff FDR Estimation There are several ways to calculate FDR depending on the database search type. In Proline the FDR is calculated at peptide and protein levels using the following rules: * if the Search has been done on a concatenated Target/Decoy bank, FDR = 2 * nbr DecoyPSM / (nbr TargetPSM + bnr DecoyPSM ). Note: when computing PSM FDR, peptide sequences matching a Target Protein and a Decoy Protein is taken into account in both cases. text/html 2015-10-29T10:19:17+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:lcmslabelfreequantitationconfig&rev=1446110357&do=diff Label-free LC-MS quantitation configuration Here is the description of the parameters that could be modified by the user. Feature extraction Strategy Defines the algorithms and methods to used for signal extraction and deistotping. * Start Extraction from XIC from : text/html 2014-10-14T13:25:34+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:lcmslabelfreequantitationworkflow&rev=1413285934&do=diff Label-free LC-MS quantitation workflow Analyzing Label-free LC-MS data requires a series of algorithms presented below. Figure 1 : overview of the differents stages of label-free LC-MS data processing 1. Generation of the LC-MS maps LC-MS maps can be imported from files generated by others peak picking LC-MS tools, or directly created through Proline with its own feature extraction algorithms. text/html 2014-10-10T16:44:10+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:lcmsquantitation&rev=1412952250&do=diff LC-MS quantification Different strategies for quantitative analysis Although 2D-gel analysis has been a pioneer method in this field, it has been gradually replaced by nanoLC-MS/MS analysis allowing nowadays to quantify a larger number of proteins and allowing their identification. Quantification is made on thousands of species and requires new and adapted algorithms for the processing of complex data. Two major strategies are available to perform nanoLC-MS/MS relative quantification: strateg… text/html 2015-02-06T11:36:03+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:lcmsquantitationadvancedconfig&rev=1423218963&do=diff Post-processing of LC-MS quantitative results This procedure is used to compute ratios of peptide and protein abundances. Several filters can also be set to increase the quality of quantitative results. Here is the description of the parameters that could be modified by the user. text/html 2014-10-10T14:04:09+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:lcmsquantitationworkflows&rev=1412942649&do=diff LC-MS quantification workflows LC-MS quantification algorithms implemented in Proline are based on the prototype software Prosper developed by IPBS. There are a large number of LC-MS map generation tools. However there was no software solution, until Prosper, able to read and compare data generated by different tools. It was thus a tedious work to evaluate the relative performance of the available peak picking solutions. Proline overcomes this problem by implementing the Prosper’s parsers in or… text/html 2015-07-10T15:22:47+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:mergeresultsets&rev=1436534567&do=diff Merger Search Results Merging several Search Results consist in creating a parent Search Result which will contain all merged PSMs issued from child Search Result. For each identified peptide (in at least one child), a single merged PSM will be created and filled with the best child attributes (score, missed cleavage, etc.). The best child PSM is the PSM with the higher score. text/html 2016-07-01T08:00:50+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:mergeresultsummaries&rev=1467352850&do=diff Merge Identification Results This merge operation consist in creating a parent Identification Result from few child ones. A Search Result corresponding to this parent Identification Result will be generated . Concretely, the first step of this merge operation consist in creating merged PSMs for all peptides identified and validated in at least one child text/html 2014-10-10T14:01:41+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:mzdbprocessing&rev=1412942501&do=diff mzDB-processing Purpose Extracting peptidic signals (called “features”) from a file converted into the mzDB format. Feature extraction algorithms The FeatureExtractor algorithm is composed of four different extraction strategies: * UnsupervisedFeatureExtractor (NYI) text/html 2015-07-10T15:20:24+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:peptidematchesfilteringandvalidation&rev=1436534424&do=diff Peptide Matches Filtering Peptide Matches identified in search result can be filtered using one or multiple predefined filters (describes here after). Only validated peptide matches will be considered for further steps. Basic Score Filter All PSMs which score is lower than a given threshold are invalidated. text/html 2013-11-13T16:42:44+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:prolinewebinstall&rev=1384357364&do=diff Proline Web installation procedure text/html 2015-07-10T15:21:05+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:proteininferer&rev=1436534465&do=diff Protein Inference All peptides identifying a protein are grouped in a Peptides Set. A same Peptides Set can identify many proteins, represented by one Proteins Set. In this case, one protein of this Protein Set is chosen to represent the set, it is the text/html 2015-06-30T15:39:55+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:proteinsetsfilteringandvalidation&rev=1435671595&do=diff Protein Sets Filtering Filtering applied during validation is the same as protsetfiltering Protein Sets Validation Once pre-filters (see above) have been applied, a validation algorithm can be run to control the FDR. See how FDR is calculated At the moment, it is only possible to control the FDR by changing the Protein Set Score threshold. Three different text/html 2015-07-10T15:21:35+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:protscoring&rev=1436534495&do=diff Proteins and Proteins sets scoring There are multiple algorithms than could be used to calculate the Proteins and Protein Sets score. Proteins score are computed during the importation phase while Protein Sets score are computed during the validation phase. text/html 2016-07-07T14:26:08+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:protsetfiltering&rev=1467894368&do=diff Protein Sets Filtering Any Identification Summary, generated by validation or merging could be filtered. Filtering consist to invalidate Protein Sets which doesn't follow specified criteria. Invalidated Protein Sets are not been taken into account for further algorithms or display. text/html 2016-07-07T14:13:28+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:pwd&rev=1467893608&do=diff Installation and configuration of Proline Web Desktop * The Proline Web eXtension (PWX) is based on the use of MongoDB database engine. You need to download it and install it either on the computer which will host the PWX server, or any other network-accessible computer. You will find the installation files on this page : text/html 2015-02-05T16:12:23+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:quantitionconfig&rev=1423149143&do=diff Quantitation : configuration The first quantitation step as well as the advanced quantitation (see quantitionprinciple) have some parameters that could be modified by the user. * Label-free LC-MS quantitation configuration * Advanced Quantitation (Profilizer) configuration text/html 2015-02-05T16:08:40+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:quantitionprinciple&rev=1423148920&do=diff Quantitation : principles This section will describes in details the quantitation principles and concepts. * LC-MS quantification: Different strategies for quantitative analysis * LC-MS quantification workflows : Workflow and implementation in Proline * mzDB-processing : Extracting peptidic signals from a file converted into the mzDB format text/html 2015-07-10T11:14:49+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:resultfile&rev=1436519689&do=diff Result File A Result File is the file created by a search engine when a new search is submitted. OMSSA (.omx files), Mascot (.dat files) and X! Tandem (.xml files) search engines are currently supported by Proline. A first step when using Proline is to import Result Files through text/html 2016-07-07T14:19:26+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:rs&rev=1467893966&do=diff Search Result A Search Result (aka ResultSet in the database schema) is the raw interpretation of a given set of MS/MS spectra given by a search engine or a de novo interpretation process. It contains one or many peptides matching the submitted MS/MS spectra ( text/html 2015-07-10T11:02:55+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:rsm&rev=1436518975&do=diff Identification Summary An Identification Summary (aka ResultSummary) is a set of identified proteins inferred from a subset of the PSM contained in the Search Result*. The subset of PSM taken into account are the PSM that have been validated a filtering process (example: PSM fulfilling some specified criteria such as score greater than a threshold value). text/html 2015-07-10T11:05:06+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:rsvalidation&rev=1436519106&do=diff Validation Algorithm Once a result file have been imported and a search result created, the validation is performed in 4 mains steps : * Peptide Matches filtering and Validation * Protein Inference (peptides and proteins grouping) * Protein and Proteins Sets scoring * Protein Sets Filtering and Validation Finally, the Identification Result issued from these steps is stored in the identification database. Different validation of a Search Result can be performed and a new Identification… text/html 2016-07-07T15:18:33+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:spectralcountdef&rev=1467897513&do=diff Compare Identification Summaries with Spectral Count Definition * The peptide spectral count consist in counting the number of spectra which matches the current peptide. Thus, it's equal to the number of peptide spectrum matches (PSM). * Protein basic spectral count text/html 2015-07-10T15:16:49+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:start&rev=1436534209&do=diff Proline Concepts & Principles * Dataset types: * Result File * Search Results * Decoy Searches * Identification Summary * Data Processing: * Protein Inference * Protein and Proteins Sets scoring * FDR Estimation * Validation Algorithm * Protein Sets Filtering * Merge multiple Search Results * Merge multiple Identification Summaries * Compare with Spectral Count * Quantitation (Principle) * LC-MS quantification * LC-MS quantification workflows … text/html 2015-03-31T14:51:21+0200 Anonymous (anonymous@undisclosed.example.com) http://biodev.extra.cea.fr/docs/proline/doku.php?id=prolineconcepts:xlsexport&rev=1427806281&do=diff Identification Summary Export When exporting a whole Identification Summary in excel file, the following sheets may be generated (depending on options) : * search settings and infos : Contains information on project and search settings parameters