Vanderbilt University Medical Center

Supporting Tool Suite for Production Proteomics

ScanSifter

Overview

ScanSifter is a data conversion tool to transcode and filter mass spectra. It reads and writes a variety of formats via use of the ProteoWizard library. Currently it supports spectral data in proprietary formats from Bruker and Thermo; adding other formats supported by ProteoWizard requires few changes. It exports data in mzML, mzXML, mzData, MGF and DTA formats. It can also translate files from MGF or XML-based formats to the others.

Two versions of ScanSifter are included in the distribution package: ScanSifter Web and ScanSifter Desktop. The former is installed in a Microsoft IIS server to provides web services that read input files from designated network directories. Alternatively, it can be configured to read a BUS database and find archived raw files automatically. The converted files are stored in file servers and subsequently processed by identification tools. ScanSifter Web can coordinate the use of shared file servers among multiple labs. If multiple ScanSifter jobs are submitted at the same time, they will be queued for processing.

 

Requirements

· ScanSifter Desktop—Windows 2000 or higher computer; 2008 C++ Redistributable; Thermo MS File Reader (for reading in Thermo RAW files)

· ScanSifter Web—Windows PC or Server 2000 or higher; IIS 5 or higher; 2008 C++ Redistributable; Thermo MS File Reader (for reading in Thermo RAW files); Oracle Client 10g or higher, or free Oracle Express Edition (if Oracle DB is running on different machine than ScanSifterWeb)

 

Installation Instructions

Summary

ScanSifter Web:

· Create the Oracle database using the provided script.

· Install the Oracle client (if necessary).

· Obtain and install the Thermo MS File Reader.

· Install the Visual C++ 2008 redistributable.

· Create the website and application pool in IIS using the provided videos.

· Install ScanSifterWeb as demonstrated in the videos.

· Install ScanSifterService as demonstrated in the videos.

· Install ScanSifterConsole as demonstrated in the videos.

· Edit the web.config file accordingly

· Edit the scansifterconsole.exe.config file accordingly.

· Open the Oracle DB table “TBLSCANDENSERUSERS” and add the user IDs (Active Directory user accounts) of people needing access to the application. You will also need to fill in the lab and email address for each user. NOTE: This application was designed around using Active Directory domain authentication for sign-on. It will have to be adapted for environments not utilizing Active Directory.

· As stated in the readme file in the ScanSifterDocuments directory, you will have to accept the license agreement for Proteowizard by using one of the two methods presented. Once completed, queue up a run in the web interface to test that everything is set up correctly.

ScanSifter Desktop:

· Obtain and install the Thermo MS File Reader.

· Install the Visual C++ 2008 redistributable.

· Run the setup.exe and install the application.

 

Details

Full installation details can be obtained in the ScanSifterDocuments directory in the distribution package or here, including

· Step-by-step video installation instructions for ScanSifter Web

· ScanSifter database setup

· ScanSifter Service configuration