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Contents 1 Prequips Inclusion List Builder Extension 1.1 About 1.2 Download 1.2.1 Software 1.2.2 Sample Data 1.3 Prerequisites 1.4 Installation 1.5 Tutorial Screencasts 1.6 Screenshot Gallery

Prequips Inclusion List Builder Extension

About

The Prequips Inclusion List Builder Extension is a plug-in for Prequips. The Inclusion List Builder facilitates a directed LC-MS/MS that decouples peak detection and sequencing of selected precursor ions. The method has been described in detail in Schmidt A, Gehlenborg N, Bodenmiller B, Mueller L, Domon B and Aebersold R, "An integrated, directed mass spectrometric approach for in depth characterization of complex peptide mixtures." (submitted).

The Inclusion List Builders supports creation of inclusion lists and subsequent mapping of identified peptides to features.

Download

Software

We currently provide the Inclusion List Builder only bundled with Prequips.

• Download for Windows: Prequips 0.96 + Inclusion List Builder
• Download for Mac OS X: Prequips 0.96 + Inclusion List Builder

Sample Data

(to come)

Prerequisites

1. Make sure you have installed and configured a Java Runtime Environment (JRE) version 1.5 or later. Most machines should have this installed by default. Should your machine not have a recent JRE installed you may download a more up-to-date version from http://java.sun.com.
2. Prequips requires large amounts of memory. We recommend at least 1024 MB.

Installation

1. Extract the downloaded Prequips ZIP archive into a directory of your choice. A new subdirectory named "prequips_xxx" will be created ("xxx" will be replaced by the version and the OS identifier, e.g. "macosx" or "win32").
2. Execute the Prequips application (prequips.app, prequips.exe, ...). A splash screen should appear within a few seconds.

Tutorial Screencasts

These tutorials require the free Apple Quicktime Player: http://www.apple.com/quicktime.

1. How to create a new project.
2. How to create the master table.
3. How to create an inclusion list.

Screenshot Gallery

The screenshots in this gallery are meant to give potential users an impression of what the user interface will look like (even though it's still in beta). This is by no means a complete overview of all features and the presented features are in shown in no particular order.

Loading an alignment using a so-called "alignment provider". Currently there are alignment providers for Superhirn (tabular format)and SpecArray. Providers for other tools or formats (i.e. Superhirn XML format) can be added easily (once they are implemented ...).	Create a new inclusion list from the features shown in the master table (big table on the top right). Filters (as shown on the bottom right) are used to select only features fulfilling specified criteria from the overall list of features.	Assign feature in selected inclusion list to segments.	Modify the settings of a filter. A filter can also be negated.
Modify the mode of a "meta filter". A meta filter combines several regular filters using a logical operator (AND, OR, XOR). There can be additional meta filters (using different operators). However, meta filters are always combined using AND, i.e. a feature has to pass every meta filter to be included in the filtered list.	All inclusion lists created from the master table, which is represented by the top entry called "Superhirn Alignment" (technically the master table is an inclusion list as well). Some preliminary statistics are shown. This will be extended.