Protein Identification

The AB SCIEX TripleTOF^TM 5600 system provides several powerful workflows for protein identification.

In the Explore workflow, the TripleTOF 5600 system acquires as many MS/MS spectra as possible without sacrificing resolution, mass accuracy, or dynamic range - up to 50 in a second using SmartSpeed^TM Acquisition. This fast acquisition rate is possible because of the high sensitivity of the instrument and is especially useful for exhaustive protein identification from extremely complex samples. The comprehensive ProteinPilot^TM Software can then be used for protein identification, taking advantage of its 'Thorough' search mode in order to identify as many of the MS/MS spectra as possible.

Fig 1: High quality MS/MS data yields higher specificity during database searching. Highlighted here, MS/MS resolution across the mass range is maintained even at fast acquisition rates where the y1 ions of Lys and Glu can easily be resolved.

+ View Larger

In the Profile workflow, the TripleTOF^TM 5600 system is set up to provide both qualitative and quantitative data all in a single run using high resolution MS data for quantitation and MS/MS data for identification/confirmation - even when fast chromatography is used. When monitoring proteins and peptides across multiple samples, the Protein Quantitation MicroApp in PeakView^® Software can be used to generate MS peak extracted ion chromatograms for quantitation.

Fig 2: Extracted Ion Chromatograms for the peptides from one specific protein using the Protein Quantitation MicroApp.

+ View Larger

The AB SCIEX TOF/TOF^TM 5800 system provides rapid in-depth protein identification from LC/MALDI and gel-spot workflows.

The AB SCIEX TOF/TOF^TM 5800 System integrates a 1kHz variable rate laser, continuous stage motion, and the DynamicExit^TM Algorithm software for faster, more reliable, in-depth data acquisition. The DynamicExit^TM Algorithm increases the speed of acquisition by advancing to the next MS/MS experiment once sufficient fragmentation data has been collected for confident identification. This minimizes wasted acquisition time and sharply reduces the sample consumption rate allowing for greater depth of coverage.

Fig. 3: The DynamicExit^TM Algorithm results in a decrease in acquisition time and sample consumption leading to more protein and peptide identifications at high confidence levels.

+ View Larger

ProteinPilot^TM Software for Protein Identification and Expression Analysis

ProteinPilot^TM Software enables fast protein identification and relative quantitation. The software enables protein identification by searching parent and fragment ion masses against a protein database and can search for hundreds of modifications, missed cleavages, substitutions and isoforms - all simultaneously. ProteinPilot^TM software incorporates the Paragon^TM database search engine, and is compatible with the MASCOT® search engine from Matrix Science. The software also incorporates the powerful Pro Group^TM algorithm for results compilation and supports ICAT®, iTRAQ® and SILAC^TM reagents workflows.

Fig. 1: The Protein Quant view in ProteinPilot^TM Software enables you to easily navigate the protein quantitation information. Color-coded protein ratios highlight differentially expressed proteins. Additionally, a single click displays the MS or MS/MS quantitation evidence for each peptide.

One combination of offerings to help you perform protein identification analysis is below:

Instruments

		AB SCIEX TripleTOFTM 5600 System: The AB SCIEX TripleTOFTM 5600 System is the only accurate mass instrument with the speed and sensitivity of a triple quadrupole providing users with the ability to achieve high sensitivity quantification and advanced qualitative capabilities for rapid protein identification and quantitation all on a single platfom.
		AB SCIEX TOF/TOFTM 5800 System: The AB SCIEX TOF/TOFTM 5800 System provides the most sensitive and confident path for MALDI mass spectrometry protein identification and expression analysis. It offers superior MS/MS capabilities for the most confident identifications of peptides and proteins from 1D and 2D gel spots or LC/MALDI workflows.

Software

ProteinPilotTM Software: ProteinPilotTM Software is a data processing tool for the protein identification and expression analysis of proteins from LC/MS/MS, LC/MALDI and gel based experiments. ProteinPilotTM Software supports all AB SCIEX platforms as well as other platforms using MGF (MASCOT® Generic Files) format.

View brochures, technical notes, webinars and videos about how we can help you with your protein identification research.

Media

Brochures

• Brochure: AB SCIEX TripleTOF^TM 5600 System: High resolution quant and qual.

• Brochure: AB SCIEX TOF/TOF^TM 5800 System: The speed and sensitivity to expand protein discovery.

• Brochure: ProteinPilot^TM Software: In depth protein identification and expression analysis.

Technical Notes

• Tech Note: In-Depth Qualitative Analysis of Complex Proteomic Samples Using High Quality MS/MS at Fast Acquisition Rates. Using the Explore Workflow on the AB SCIEX TripleTOF^TM 5600 System.

• Tech Note: Simultaneous Peptide Quantification and Identification using High Resolution MS. Using the Profile Workflow on the AB SCIEX TripleTOF^TM 5600 System.

• Tech Note: Quantitative Protein Profiling in Cell Signalling Networks. TOF MS Profiling using the AB SCIEX TripleTOF^TM 5600 System.

• Tech Note: Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests. AB SCIEX TOF/TOF^TM 5800 System with DynamicExit^TM Algorithm and ProteinPilot^TM Software for Robust Protein Identification.

• Tech Note: Improved Depth of Coverage for Single Spot Analysis. DynamicExit^TM Algorith on the AB SCIEX TOF/TOF^TM 5800 System.

• Tech Note: Top-Down Sequencing of Intact Proteins by MALDI In Source Decay (ISD). Protein Characterization using the AB SCIEX TOF/TOF^TM 5800 System.

• Tech Note: Identification of Disulfide-Linked Peptides by LC-MALDI Using Extracted Fragment Chromatograms. Protein Characterization using the AB SCIEX TOF/TOF^TM 5800 System.

• Tech Note: Assessing the Complementarities of MALDI and ESI for Protein Identification in Complex Mixtures. Comparing the AB SCIEX TOF/TOF^TM 5800 System with the ESI Orbitrap using ProteinPilot^TM Software.

• Tech Note: Biomarker Discovery in the Time Dependent Progression of Lung Fibrosis. AB SCIEX 4800 Plus TOF/TOF^TM Analyzer with iTRAQ&Reg; Reagents-8plex and ProteinPilot^TM Software Provides an Integrated Solution for Protein Quantification in Large Datasets.

• Tech Note: ProteinPilot^TM Descriptive Statistics Template (PDST). Powerful Analysis Tools for Protein Identification Results from ProteinPilot^TM Software.

Webinars

• AB SCIEX TripleTOF^TM 5600 System: Next Generation Performance for Proteomics Research.

• Effects of Intelligent Data Acquisition and Fast Laser Speed on Analysis of Complex Protein Digests.

• The Paragon^TM Algorithm for the Identification of Native (Non-Trypic) Peptides.