hEIDI how_to

how_to:accessadjustedspectralcountdata

Anonymous (anonymous@undisclosed.example.com) — 2013-01-28T15:31:11+0200

How to run and access adjusted spectral (ASC) count data See spectralcount for more details on the algorithm and parameters. Run the ASC algorithm * Select one or more context of your choice (for which protein grouping have been executed) * Right-click and select

how_to:accessidentificationinfos

Anonymous (anonymous@undisclosed.example.com) — 2010-07-23T13:20:21+0200

How to access identification general informations (parse parameters, filters, statistic, FDR,...) You can retreive all informations related to an identification result from its properties. Identification results are visible either in the Identifications window or in the MSIExplorer window.

how_to:accessproperties

Anonymous (anonymous@undisclosed.example.com) — 2010-07-26T10:51:41+0200

How to access object properties Properties are characteristics attached to a given “object”. Most of the time these objects are represented by “nodes” in a tree view. There are several ways to access object properties: * in a property sheet * in a tree view where the columns often

how_to:accessspectralcountdata

Anonymous (anonymous@undisclosed.example.com) — 2012-02-29T12:26:33+0200

How to run and access spectral count data :!: Since hEIDI 1.13.0, spectral count has been tuned. To achieve this, the new field leaves_match_count in MSIdb has been created in the peptide_instance table. For this reason, an MSIdb migration has to be realized to add & populate this field if you intend to use the hEIDI 1.13.0 version.

how_to:alignretentiontime

Anonymous (anonymous@undisclosed.example.com) — 2010-08-04T12:11:49+0200

How to align retention time See Retention Time Alignment principles if needed. Run the Retention Time Alignment algorithm [Retention Time Alignment menu] :!: Required condition to run the Retention Time Alignment algorithm: * Selected User context must be grouped If above condition is respected, then follow these steps:

how_to:batchprocessing

Anonymous (anonymous@undisclosed.example.com) — 2012-01-23T15:54:09+0200

How to make a batch processing Batch processing lets you link together several algorithm and filters. Available process are : * Algorithms * protein grouping * compute spectral count data (Can only be done if selected contexts are grouped or if protein grouping is done before in the batch)

how_to:browsecontextprotgroups

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T14:21:08+0200

How to browse context's protein groups [Protein groups for a given Context] * Right-click on a context of your choice (for user context, protein grouping should have been executed) in the MSIExplorer window and select “Browse->Protein groups” in the context sensitive menu * Browse

how_to:changetypicalprotein

Anonymous (anonymous@undisclosed.example.com) — 2010-03-16T14:52:05+0200

How to change typical protein Filtering can be done on 1 or more User Context. Once desired contexts are selected, you can * Right-click on contexts in MSI database ans select Algorithms -> Change typical protein * Or choose MS Identification –> Context –> Algorithms

how_to:comparecontextwithextaccession

Anonymous (anonymous@undisclosed.example.com) — 2010-10-28T15:10:44+0200

How to compare a context with an external accession list The purpose is to compare a list of protein accession from a text file, to all proteins contained into a Access * Select a context (Search context or grouped User context) * Right-click and select

how_to:comparemulticontexts

Anonymous (anonymous@undisclosed.example.com) — 2012-02-28T11:39:24+0200

How to compare multiple contexts See here for more details about comparison result view and concepts. You can compare : * an existing parent union context with its children, * or several contexts with a *virtual* parent union :!: Activation conditions

how_to:comparemultiplecontexts

Anonymous (anonymous@undisclosed.example.com) — 2010-01-04T17:04:53+0200

How to compare a context with its children [Compare a context with its children] * Select the context of your choice (protein grouping needs to be previously executed for this context and its childs) * Right-click and select “Algorithms→Compare with→Children” * The comparison window display the result

how_to:comparetwocontexts

Anonymous (anonymous@undisclosed.example.com) — 2010-01-06T14:23:07+0200

How to compare contexts each other [Compare contexts each other] * Select the two contexts you want to compare each other. The contexts may be a Search Context or a User Context (for which protein grouping has been previously executed) * Right-click and select “Algorithms->Compare with->Each Other” * The comparison window display the result

how_to:computefalsepositiverate

Anonymous (anonymous@undisclosed.example.com) — 2012-02-27T19:27:32+0200

How-to compute False Positive Rate See here to have more details about False Positive Rate calculation. Run the False Positive Rate algorithm :!: Required condition to run the False Positive Rate algorithm: * Selected User context must be grouped

how_to:createcontext

Anonymous (anonymous@undisclosed.example.com) — 2010-01-05T16:29:20+0200

How to create a new context to organize and compile identification results In the MSIExplorer window: * Right-click on the User Context node and select New Context to create the “Root node” of your tree. * Select this new node and press F2 to rename it (or right-click on it and select

how_to:createproject

Anonymous (anonymous@undisclosed.example.com) — 2009-12-16T09:16:14+0200

How to create an hEIDI Project An hEIDI project is always associated to a MSIdb connection. You should have created a MSIdb connection before to create a new project. In File Menu or Project tab context menu : * select New Project * in step 1., choose the Heidi Project and click next

how_to:dbconnection

Anonymous (anonymous@undisclosed.example.com) — 2016-08-24T15:38:34+0200

How to create a connection to a database In order to use hEIDI, a connection to a MSI db (Mass Spectrometer Identification database) is required. But it is possible to create a connection for all kind of databases and to execute queries on it. In the

how_to:deletecontext

Anonymous (anonymous@undisclosed.example.com) — 2011-07-22T16:22:32+0200

How to delete context(s) Delete Search context(s) From the MSIExplorer window: * Select the Search context(s) you want to delete (multiple selection allowed) * Right-click to display context menu and choose Delete... [How to delete Search context(s)] Delete User context(s) From the MSIExplorer window,

how_to:editidentificationinfos

Anonymous (anonymous@undisclosed.example.com) — 2010-07-26T14:21:24+0200

How to edit identification properties [ ] To edit properties (general properties or associated Run and Sample) of an identification : * select the identification to get information for * right click * choose Edit in popup View The edit windows is divide into 2 parts : Runs and sample informations and properties details. See more information on

how_to:exportadhocexport

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T17:20:19+0200

How-to export data (Ad-hoc export) As the number of customized exports keep on increasing, a new way to export data has been implemented to answer users'needs more easily & quickly. :!: You can still export data using MS Identifications->Context->Export

how_to:exportadhocexport_n15

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T17:19:49+0200

How-to export N15 quantitation data See also exportadhocexport * From the MSIExplorer view, select the UserContext node to export 15N data from * Select MS Identifications->Context->Export->Data from the main menu bar, to display the Export Data dialog * Select

how_to:exportadhocexport_ppmswleaves

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T18:00:28+0200

How-to export Protein Groups, their peptides and their leaves See also exportadhocexport Run the Export Data feature * From the MSIExplorer view, select the UserContext node to export data from * Select MS Identifications->Context->Export->Data from the main menu bar, to display the

how_to:exportcomparison

Anonymous (anonymous@undisclosed.example.com) — 2011-02-01T10:19:46+0200

How to export comparison result Only one Graphical User Interface now exists to display context comparison results. At present, no export is available to user. In order to have data in a excel file: * Press Ctrl+A to select all cells * Ctrl+C to copy data

how_to:exportcontext

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T18:33:26+0200

How to export identified peptides & proteins from a context How to access this feature * Select the context of your choice (for a User context, protein grouping should have been executed) in the MSI Explorer window * Click on the menu MS Identification > Context > Export > Reports

how_to:exportpride

Anonymous (anonymous@undisclosed.example.com) — 2013-01-28T08:05:01+0200

How to export a UserContext into the PRIDE XML Format Warning: * :!: Exporting a UserContext to PRIDE XML format is only available for MSIdb version D.4 (or later versions). * :!: In hEIDI versions v1.10.1, v1.11.0 and up to now (MSIdb E.1), the header

how_to:exportpridelog

Anonymous (anonymous@undisclosed.example.com) — 2011-12-05T15:55:14+0200

How-to view PRIDE log When exporting to PRIDE XML format: * PRIDE messages having ERROR severity are displayed in the hEIDI console * ALL PRIDE messages (DEBUG, INFO, ERROR...) are displayed in a separated file (pride.log) at the hEIDI root :!:

how_to:exportsqlresult

Anonymous (anonymous@undisclosed.example.com) — 2010-02-03T11:35:31+0200

How to export an SQL result to a file If needed, see how to write SQL query. * You can increase the number of visible rows in the table by entering a number of lines in the Page size text edit. The refresh the view by using the blue Refresh records icon. * select one row, then

how_to:fillidentinfo

Anonymous (anonymous@undisclosed.example.com) — 2010-07-26T10:51:01+0200

How to retrieve Sample/Run informations from ePims Identifications, runs and samples are associated. [ ] To retrieve these informations from ePims data (registered as acquisition and sample) : * select one or more identifications to get information for * right click * choose

how_to:generateamtdb

Anonymous (anonymous@undisclosed.example.com) — 2012-02-29T12:30:37+0200

Generate a new AMT database from a context :!: Requirements * Context have to be grouped previously. You generally apply some filtering during and/or after the protein grouping step to suppress: * Reverse proteins * Species with a sequence < 7

how_to:graphicalplotpeptides

Anonymous (anonymous@undisclosed.example.com) — 2010-01-04T17:02:50+0200

How to generate a graph (histograms, plots, ...) on peptides features With hEIDI, you can easily plot a graphical representation of the peptides contained in one more more contexts. You can choose the type of plot the most appropriate to your needs (histogram, scatter plot or matrix, parallele, bubble plot, etc).

how_to:idffilters

Anonymous (anonymous@undisclosed.example.com) — 2010-01-06T14:22:42+0200

How to check that all identifications have been filtered with the same parameters To check if your identification results have been filtered in the same way: * Go the the Identifications tab (you can retreive it from the main menu Window > Identifications

how_to:importumctomsidb

Anonymous (anonymous@undisclosed.example.com) — 2012-03-15T08:45:31+0200

How-to import UMC result files into the MSIdb See also more details about UMCs import into MSIdb :!: Requirements: * An AMT database had to be previously created from one User context in the current opened MSI database Access menu * Don't select any context (actually, select the User context category node) * Select MS Identifications

how_to:includeumcinamtdb

Anonymous (anonymous@undisclosed.example.com) — 2010-08-02T16:57:42+0200

How to integrate UMCs information into AMTdb Run the ''Read UMCs'' tool It is not necessary to open an hEIDI project to launch this tool. Just click on Tools->Read UMCs from the main menu bar. Tool options * Add ePims Web Server URL * The ePims WebService is used to extract Sample information from Run name

how_to:loadproject

Anonymous (anonymous@undisclosed.example.com) — 2010-01-04T16:58:51+0200

How to reopen en existing hEIDI Project If you created a project with an other hEIDI or your project is no more referenced in hEIDI, it is possible to load an existing project : In File Menu or Project tab context menu : * select Open Project *

how_to:opensession

Anonymous (anonymous@undisclosed.example.com) — 2010-01-04T17:00:34+0200

How to open an MSI Session MSI session can be opened for any hEIDI project, see how to create an hEIDI Project for more information. An MSI session should be opened in order to be able to explore a MSI db content. This could be done in one or two few steps. * Activate hEIDI Project

how_to:peptideview

Anonymous (anonymous@undisclosed.example.com) — 2012-02-28T17:08:43+0200

Visualize all context's peptides See more details about peptide view. You can visualize all peptides contained in any given Search or User context (for a User context, protein grouping has to be executed first): * Right-clik on the context node of your choice. * Select Browse > Peptides

how_to:proteinfiltering

Anonymous (anonymous@undisclosed.example.com) — 2012-01-23T14:50:55+0200

How to filter proteins or protein groups Filtering can be done on 1 or more User Context. Once desired contexts are selectedn right-click in MSI database ans select Proteins Filters window or choose MS Identification --> Context --> Proteins Filters

how_to:proteingrouping

Anonymous (anonymous@undisclosed.example.com) — 2012-01-23T14:29:05+0200

How to group proteins within a context Grouping is automatically saved to MSIdb. For more information on protein grouping, see here. Load menu [Execute protein grouping] * Right-click one ore more context nodes of your choice in the MSIExplorer view to display context sensitive menu and select

how_to:recomputeretentiontime

Anonymous (anonymous@undisclosed.example.com) — 2010-08-04T12:10:26+0200

How to Recompute Retention Time See Retention Time Recomputing principles if needed. :!: If you recompute retention time for a given User context, it will not automatically recompute retention time for child contexts (i.e. contexts under the selected context, if exist). :!: At present, you need to recompute retention time of all your context tree 'manually'. For that, no specific order is needed as final child species are used.

how_to:resetproteinfiltering

Anonymous (anonymous@undisclosed.example.com) — 2010-11-10T17:15:19+0200

How-to reset a protein/protein group filter

how_to:savecomparison

Anonymous (anonymous@undisclosed.example.com) — 2011-02-01T11:12:09+0200

How to save/load a comparison result Save a comparison result After having run a context comparison, results display in a window. Results can be saved in the associated hEIDI project in order to be loaded later without running the algorithm again. * Click on the save button in toolbar and wait for the following message to appear. The filename has .ucr (Union Comparison Result) as extension and is created using the names of compared contexts with an optionnal increment at the end.

how_to:savetomsidb

Anonymous (anonymous@undisclosed.example.com) — 2010-01-06T16:29:23+0200

Save modifications back to the MSIdb :!: At present, it is not possible to save a specific context back to the MSI db, all the contexts are saved. To save all the modifications back to the current MSI db, do the following steps: * Select the User context

how_to:spectrummatchfeeder

Anonymous (anonymous@undisclosed.example.com) — 2013-04-11T10:41:58+0200

How-to populate MSI database with spectrum details Before exporting a given UserContext to PRIDE XML file, check if the MSI database need to be populated with spectrum details. :!: Since hEIDI 1.11.1, this functionality is no more available from the hEIDI GUI, but has to be executed (outside from hEIDI, see bellow) [by your system administrator].

how_to:start

Anonymous (anonymous@undisclosed.example.com) — 2013-01-28T08:09:12+0200

How to Creation/Suppression * create a connection to a database * create an hEIDI Project * open a MS Identification session to explore MSIdb content * create new contexts to organize and compile identification results * reopen an existing hEIDI Project * delete context(s) * get Sample/Run informations from ePims Visualization * Browse all context's protein groups * visualize all context's peptides * visualize protein groups information details * generate a graph (hi…

how_to:viewprotgroups

Anonymous (anonymous@undisclosed.example.com) — 2010-04-14T14:11:06+0200

How to visualize protein groups information details There is few ways to access to the protein group detail page : * From Protein Groups list : right-click on ths protein group (typical) of your choice in the ContextExplorer window and select View Protein in the context sensitive menu or if a protein group window is already opened, just select a new protein group in the list.

how_to:writesqlqueries

Anonymous (anonymous@undisclosed.example.com) — 2010-02-03T11:36:40+0200

How to write SQL Queries to explore database Once you are opened an MSI session, you can explore the database by creating SQL queries. Information on MSI database and its model is available here . View data from a table It is possible to view data from a table like this: