Quantitative and Qualitative Proteomics Research Platform

ProteinLynx Global SERVER™ (PLGS) is a fully integrated Mass-Informatics™ platform for quantitative and qualitative proteomics research. It is the central analytical platform for Waters proteomics systems.

PLGS leverages the selectivity of exact mass measured data and the specificity of MS^E analysis. Combined with intelligent filtering and scoring routines, this minimizes the occurrence of false positive results.

PLGS is based on open/pluggable system architecture, providing scalable, automated workflow for your high-throughput data processing and data interpretation. PLGS also includes project and database management tools with integrated results visualization and reporting.

Import sample information and data into PLGS through XML (mzData supported), which provides integration of the PLGS toolset into a LIMS or Data Management System such as Waters NuGenesis SDMS. The PLGS custom report generation utility also allows you to produce publication-ready result reports.

Identity^E for Confident Protein Identification

PLGS features comprehensive peptide ion accounting informatics that mines deeper into your label-free UPLC/MS^E data. Identify more peptides/proteins with greater sequence coverage and statistical rigor than conventional LC/MS/MS methods.

Expression^E  for Label-free Quantitation

PLGS features XML based informatics to support complete data processing and integrated qualitative and quantitative results reporting of your labeled data, together with potential marker identification and exporting to data visualization platforms.

Multi-threaded Data Processing

The MaxEnt™ algorithms available with ProteinLynx Global SERVER™ (PLGS) maximize sensitivity and information content from your raw data by collapsing multiple isotopes and charge-states into monoisotopic peptide peaks.

Quantifying Proteins and Peptides for Biomarker Discovery

LC/MS quantification with protein or peptide labeling using the Waters Protein Expression System is ideal for large-scale studies requiring high reproducibility and accuracy. Simultaneous LC/MS^E data acquisition also provides identification of parent proteins with 100 percent peptide detection efficiency.

Identifying Proteins and Modifications (Multi-threaded)

Integrated ProteinLynx™ and MASCOT^® database searching is the method of choice to maximize number and confidence of protein identifications with exact mass MS and MS/MS data from Waters time-of-flight mass spectrometers. Waters’ AutoMod algorithm provides a rapid screening to maximize the coverage of identified dB proteins. AutoMod is integrated with both PLGS and MASCOT dB searching capability.

De novo Sequencing and Homology Searching (Multi-threaded)

To characterize and identify peptides not represented within protein databanks, the MassSeq™ routine takes advantage of the specificity afforded by exact mass MS/MS data to generate the most probable de novo peptide sequences.

Automation

The hierarchical workflow manager set-up allows you to chain together multiple algorithms to provide complete analysis through data processing, databank searching, modification analysis, de novo sequencing, BLAST homology searching and results reporting.

Project Management and Data Interchange

PLGS includes project management structure with full support for MALDI TOF MS, MALDI TOF PSD, MALDI/MS/MS, ESI/MS and ESI/MS/MS data, from 2D PAGE, 1DLC or 2DLC workflows.

Database management manages your in-house databases and automatically uploads new versions from the web or in-house servers.

Pluggable architecture and multiple file formats (XML, mzData, pkl, txt etc) enable integration with other software packages or a LIMS, so your results can be linked with orthogonal experimental data. All tools, samples, data and results are accessible thorough a single, integrated browser.

MASCOT is a trademark of Matrix Science.

Since the introduction of ProteinLynx Global SERVER 2.0, a number of versions of the platform have been released, providing new and improved tools and features to improve the quality and accessibility to qualitative and quantitative results. An upgrade to version 2.3 includes all the listed features.

PLGS 2.2.5

• Protein Quantification
• Label-free quantification
• Quantification with isotopic and isobaric labeling
• Data visualization tools
• Qualitative Identification Capabilities
• Data-independent protein identification
• Improved Data Directed Analysis (DDA™)
• Increased productivity
• Enhanced Data Interchange
• Two search engines in one browser
• Two-way 2D gel integration
• Submit your data for publication

PLGS 2.2

• Graphical report generation
• Customizable reports or choose from pre-selected templates
• Integration with MASCOT
• Query two search engines simultaneously
• Compare results side-by-side in a single window
• PSD MX™ support
• Search MALDI micro MX™ data acquired using Waters’ patented multiplexed PSD method
• Remote data processing
• Frees up your acquisition PC

PLGS 2.1.5

• Improved file system performance
• Faster and safer data handling in support of multi-sample projects and large file sizes
• Enhanced support of Q-Tof Ultima^® MALDI and MALDI Q-Tof Premier™ data files
• Search MS and MS/MS data in a single operation
• Enabled 2D-LC experiments
• Merge database search results from discrete data files

PLGS 2.1

• Implementation of Waters Protein Expression System Informatics
• Introduction of Waters’ proprietary non-labelled protein quantification system, featuring patented MS^E data acquisition
• Activation requires Protein Expression System license