hEIDI userguide

userguide:contextcomparisons

Anonymous (anonymous@undisclosed.example.com) — 2012-02-28T11:18:35+0200

Context comparisons Definition The purpose is to search for similar protein groups, i.e. protein groups: * having the same set of proteins * identified by a same set of peptides The Dice coefficient is used to measure similarity (result ranges from 0 to 1).

userguide:contextdefinition

Anonymous (anonymous@undisclosed.example.com) — 2010-01-05T12:11:43+0200

Context Definition Context is a central notion in hEIDI. Basically, it contains identification results, i.e. a set of proteins identified by a set of peptides. There are two types of contexts in hEIDI: * Search context: each identification result from Mascot, or from any other identification engine, is automatically

userguide:falsepositiverate

Anonymous (anonymous@undisclosed.example.com) — 2012-02-27T18:55:24+0200

False Positive Rate The Formula used to compute False Positive Rate is: * FPR = ∑FP/(∑TP+∑FP) * with FP = (2*reverse). This FP value is get from the “significant.and.duplicated.fp” identification property. * with TP = (reverse+forward) - FP. This TP value is get from the

userguide:heidiproject

Anonymous (anonymous@undisclosed.example.com) — 2010-01-11T16:25:31+0200

hEIDI Projects hEIDI project is the entry point for MS Identifications data exploration and visualization. In order to work on identifications data, the first step is to create an hEIDI Project. Most of the MSI information is stored in the project's database. But there are still some validation result and expertise data that are not saved in the database, these data are stored in the hEIDI project. Theses informations are : contexts comparison result (on which validation could have been done)…

userguide:identrunsample

Anonymous (anonymous@undisclosed.example.com) — 2010-07-26T10:55:05+0200

Identifications, runs and samples Definition Identification result issued from a search engine, such as Mascot(r) server and validated by user are represented by Identification. These identifications could have been done on 1 peak list or on a merged peak list.

userguide:peptidesandproteingrouping

Anonymous (anonymous@undisclosed.example.com) — 2012-03-29T09:02:16+0200

Protein grouping Protein grouping is done from a parent context and consist of * creating new peptides (grouped peptide) ans matches from the union of all peptides referenced in child context (direct child if exist, otherwise more deeper childs).

userguide:pride_converter

Anonymous (anonymous@undisclosed.example.com) — 2011-03-04T18:17:00+0200

PRIDE Converter PRIDE Converter is available at * Dowload the PRIDE_Converter_vX.Y.Z.zip file, then unzip. * To execute PRIDE Converter, double-click on PRIDEConverter-X.Y.Z.jar PRIDE Converter converts mass spectrometry data from most common data formats (MASCOT .dat file for example) into PRIDE XML.

userguide:pride_export_properties

Anonymous (anonymous@undisclosed.example.com) — 2011-03-08T14:37:01+0200

More details about PRIDE XML format & runDescriptor.properties PRIDE (PRoteomics IDEntifications database) is a public data repository for proteomics data. PRIDE XML is the file format used for submission to the publicly available PRIDE database. The PRIDE XML schema documentation is available

userguide:pride_inspector

Anonymous (anonymous@undisclosed.example.com) — 2012-03-14T12:06:14+0200

PRIDE Inspector PRIDE Inspector is an application to visualize and perform a first quality assessment of MS data. With PRIDE Inspector users can have a close look at their own data before the actual submission, or access data already in PRIDE for data mining purposes.

userguide:properties

Anonymous (anonymous@undisclosed.example.com) — 2010-07-26T10:45:15+0200

Properties Properties are characteristics attached to a given “object”, such as an Identification, a Context, a Protein Group, a Run or a Peptide. See how to access properties. Properties are organized in groups. For example, identifications properties are organized into

userguide:proteinfiltering

Anonymous (anonymous@undisclosed.example.com) — 2010-11-05T11:08:46+0200

How-to filter proteins or protein groups On a User Context it is possible to apply filters. Filter will mark as hidden (or masked) protein groups or proteins inside protein groups (depending on user choice) according user defined criteria. * If protein groups are filtered (i.e.

userguide:proteingroups

Anonymous (anonymous@undisclosed.example.com) — 2012-02-28T16:22:43+0200

Protein Groups and peptides See also how-to access the protein group view and/or how-to access peptide views. Definition A Protein Group (similar to Mascot® protein hit) is a collection of proteins identified by a set of peptides. A Protein Group contains not only all proteins covered by the same set of peptides but also all proteins covered by a subset of these peptides. In details, a Protein Group:

userguide:retentiontimealignment

Anonymous (anonymous@undisclosed.example.com) — 2010-08-02T16:27:05+0200

Retention Time Alignment Major steps followed by the Retention Time Alignment algorithm * Collect species from the reference User context and predict their retention time using an external utility and store them in reference species properties

userguide:retentiontimerecomputing

Anonymous (anonymous@undisclosed.example.com) — 2010-08-02T16:49:43+0200

Retention Time Recomputing Steps followed by the Retention Time Recomputing algorithm * For each 'parent' species from the selected User context (i.e. User context for which RT Recomputing is needed) * Collect RTs for all final child species

userguide:spectralcount

Anonymous (anonymous@undisclosed.example.com) — 2013-01-28T15:32:38+0200

Spectral count See how to run spectral count algorithm See how to run adjusted spectral count algorithm Definition The Spectral Count algorithm can be run for a given context and will loop on every protein groups of this context to calculate this property. Spectral count reflects relative abundance of a protein by counting how many times all peptides of a proteins have been fractioned.

userguide:start

Anonymous (anonymous@undisclosed.example.com) — 2012-02-29T12:28:21+0200

hEIDI User Guide Concepts * hEIDI Project * Data concepts : * Context definition * Changed :!: Protein groups and peptides * Identifications, Runs and Samples * Properties * PRIDE Export Properties * PRIDE Converter * PRIDE Inspector * Operations definitions * Grouping peptides and proteins * Filter proteins [groups] * Changed :!: Contexts comparison * Changed :!: Spectral Count * Retention time alignment * Retention time recomputing * …

userguide:umctomsidb

Anonymous (anonymous@undisclosed.example.com) — 2012-03-15T10:05:32+0200

Mode details about importing UMCs to MSIdb Transfering Viper result folder(s) into MSI database: * Establish a gateway between the MSI database (PostgreSQL) and the AMT database (MS Access) * For each Viper result folder: * Check Viper folder contents