Progenesis LC-MS

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract Progenesis LC-MS (Liquid Chromatography-Mass Spectrometry) is an advanced proteomics research solution for your label-free quantitative analysis using a unique alignment based approach to give you the advantages of:

1) Speed - Reduce the time spent analyzing samples from months to days or weeks to hours. Analyze more data more rapidly to run enough replicates for reliable results.

2) Objectivity - Reduce subjective and laborious manual checking of complex data. The step-wise and guided analysis is designed to be objective and help you to reproduce results between experiments or across labs.

3) Statistics - Generate complete data sets for valid multivariate statistical analysis. This allows you to visualize and explore relationships within your complex biological data and make reliable conclusions.

You can quickly and easily visualize complex data, perform objective statistically-based differential analysis without requiring identifications and incorporate targeted LC-MS/MS data to identify proteins of interest.

Progenesis LC-MS features/capabilities include:

Data Import - Supports common formats: .mzXML, Waters .RAW, Thermo .RAW and NetCdf file formats. Peak modeling and data reduction decreases file sizes by an order of magnitude without compromising quantitative accuracy.

Data Alignment - Automatic retention time alignment allows the creation of a single “aggregate run” containing all peptide ion data from all samples.

Label Free Detection, Normalization and Quantification - A single peptide map is created containing all the peptides from all samples so they can be detected and quantified. The advanced detection algorithm handles complex samples and overlapping peptides, while accurate quantitation and normalization enables confident differential analysis.

The fully automatic analysis process produces high quality and complete datasets that allow robust, statistical analysis with multivariate statistical tools.

Experimental Group Setup - Multiple experiment groupings (e.g. male v female, control v treated) can be defined making it quick and easy to ask additional questions of your data.

Peptide Ion Selection - Significant peptide ions are ranked for review by fold-change and ANOVA (P-value) and can be assessed using the 1D / 2D/ 3D views and expression profiles. Any editing of detected peptides is greatly simplified as a single edit on the aggregate run is propagated across all runs.

Peptide ions can be grouped in multiple ways using the simple yet advanced tags feature which allows the exploration of complex relationships or to quickly generate inclusion lists for MS-MS identification.

Progenesis Stats - An advanced, easy-to-use multivariate statistical analysis tool for confident data exploration and visualization. This tool allows False Discovery Control, Principal Components Analysis, Correlation Analysis and Power Analysis to be performed on your data (see G6G Abstract Number 20369).

Search MS-MS Protein Identification Database - A simple, visual way to validate and select MS-MS (tandem MS) spectra then run database searches using Phenyx (see G6G Abstract Number 20080), Mascot™ (see G6G Abstract Number 20087), or SEQUEST (see G6G Abstract Number 20285).

Your search results are imported and displayed alongside the differential analysis results. You can filter imported identifications based on peptide score.

Protein View - Bring together quantitative LC-MS data and qualitative LC- MS/MS (tandem MS) results at the protein level to define any proteins of interest between experimental groups based on expression change with ANOVA (p-value). Easily resolve conflicts where a peptide sequence is associated with more than one protein as a result of a database search (see below...).

Report Results - Aggregate run displayed to show the location of selected peptides of interest. Report and export all peptide and protein measurements, including raw data to calculate spectral counts, for further data mining.

Progenesis LC-MS v2.0 - New features:

Protein View brings together information on peptides at the protein level -- This feature allows you to easily combine quantitation and identification data at the protein level based on the peptides of interest from objective, statistically driven differential expression analysis.

The protein name, abundance (calculated from the sum of all peptide abundances from every run); fold change and ANOVA p-value allow you to define the proteins that are differentially expressed between the experimental groups of interest.

You can also validate your protein identifications based on

The Protein View also enables you to resolve conflicts where a peptide sequence is associated with one or more proteins as a result of a database search. You can display the alternative protein IDs for a selected peptide and use the views to either discount it or update it as the actual protein of interest.

Additional information available for detected peptides -- You can now view and export additional information to characterize and report on peptides -

Display and export protein information -- You can view and report information on proteins of interest from the Protein View -

Analyze data from low resolution instruments -- You can now perform LC-MS analysis on a wider range of instruments with new peak modeling and detection algorithms included for optimal analysis of data from low resolution ion trap instruments.

Additional Improvements --

System Requirements

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Manufacturer Web Site Progenesis LC-MS

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G6G Abstract Number 20368

G6G Manufacturer Number 104017