This document describes Protea's laboratory and mass spectrometry capabilities for proteomics sample analysis. It offers a variety of products for sample preparation prior to mass spectrometry, including tools for gel-based and solution-based proteomics workflows. Products cover sample isolation, fractionation, digestion, separation, and analysis steps. Services include protein identification and characterization using the company's mass spectrometers.

2. Protea’s 5,000 sq ft laboratory
features BIOiTRAQ MALDI TOF/TOF
(ABI 4800) and LTQ (Thermo) mass
spectrometers
Isolate - Fractionate - Collect - Digest - Separate - Analyze
BIOLOGY
clinical samples:
ü blood
ü tissue
ü urine
ü sputum
CHEMISTRY
Sample Analysis
by
Mass Spec
Connecting Biology to Mass Spectrometry

3. Connecting Biology to Mass Spectrometry
a new product offering
Products for Gel-Based Proteomics and Genomics
Products for Solution-Based Proteomics
Products for Capillary Electrophoresis
Services
Isolate - Fractionate - Collect - Digest - Separate - Analyze
BIOLOGY
clinical samples:
ü blood
ü tissue
ü urine
ü sputum
CHEMISTRY
Sample Analysis
by
Mass Spec

4. The GPR Gel Protein Recovery System
Ø Recovers intact proteins from gels
Ø Removes salts, detergents and dyes
Ø Improves sample quality for downstream MS
Ø Enables top-down proteomics
Ø Elutes proteins from 5kDa to 200 kDa
Ø Quantitative protein recovery data available
Products for Gel-Based Proteomics and Genomics

5. Related Gel-Based Proteomics Products
SDSaway detergent removal
Silver Staining Kit
Protein MW Markers
Solvates SDS detergent
from the protein surface
Fast, simple - works
Ultrafast
Ultrasensitive
(20-40ng/band)
Designed for use with
Laemmli SDS-PAGE gels
From 6,500 to 200,000 Da
Products for Gel-Based Proteomics and Genomics

6. Programmable Syringe Pump
Ø Fully programmable
Ø Operates standalone or from a computer
Accessories for Sample Preparation

7. ProteaGeltm Products
Ø Ready to use
Ø No stacking gel required =
longer gel separations
Ø Stable at room temperature for one year
Ø Mass Spec Certified
Products for Gel-Based Proteomics and Genomics

8. SeaClear Agarose products
Ø Complete Line of agarose products
Ø Value Pricing
Ø Protea in-house Quality Testing
Products for Gel-Based Proteomics and Genomics

9. Proteases and ProteaBeadstm
Protea Endoproteinases
Ø Certified Mass Spec Grade
Ø Performance Tested
ProteaBeads
Ø Immobilized Trypsin & Glu-C
Ø Rapid, efficient digestion
Ø Prevents contamination of sample
with autodigestion products
Ø Available in flow-through cartridges
Products for Solution-Based Proteomics

10. MALDI sample prep
Complete kit - optimizes samples for MALDI MS
Removes Coomasie Stain bound to protein
Uses ultrapure matrix
Products for Solution-Based Proteomics
Figure 1 presents the effect of coomasie stain on the
MALDI-TOF MS signal of a Myoglobin protein sample.
The spectrum reveals different number of coomasie
molecules bound to the protein molecules as indicated by
the resolved adducts in the spectrum. This adduction of
coomasie to protein molecules results in reduced
sensitivity since the protein signal is spread over the
different adducts. In addition, the coomasie-protein
adducts can mask the presence of any post-translationally
modified protein molecules. Removal of coomasie by
destaining therefore results in an improved MS signal

11. UltraPure MALDI Matrices
Protea Ultrapure CHCA matrix
Vs. competitor
Ø Improved MALDI-MS sensitivity
Ø Forms homogenous crystals
Ø Easy reconstitution
Products for Solution-Based Proteomics

12. Reversed Phase Sample
Preparation Products
Ø C18 ProteaTips - effective for salt removal
Ø Clean-up of peptides from in-gel digested proteins
Ø C18 ProteaPlate - 96 well sample cleanup
C4 & C8 Tips also available
Supplied as kits with buffers and protocols
Products for Solution-Based Proteomics

13. Titanium Dioxide Sample
Preparation Products
For enrichment of phosphopeptides
in protein digest samples,
particularly complex protein/
peptide samples
Provided as complete kits with
sample reconstitution and
wash buffers
Also available in 96 well plates
Products for Solution-Based Proteomics

14. ZICtm HILIC ProteaTips
& Sample Prep Kit
Effective in removal of
detergents & salts
Enriches peptides complementary
To those trapped by C18 ZipTips
Low backpressure during
Sample processing
Products for Solution-Based Proteomics
Zic is a registered trade mark of Sequant AB

15. Facettm Columns for ESI Mass Spectrometry
Made of PEEK Biocompatible plastic
Trapping Columns Now Available:
Reversed Phase (RP)
Cation Exchange (CX)
ZICtm -HILIC
Also available:
FACET microfilters
Products for Solution-Based Proteomics
Zic is a registered trade mark of Sequant AB

16. Products for Capillary Surface Modification
Ø Capillary Coating Kit
Ø Reproducible control of EOF
Ø Stable for wide pH ranges
Ø Coatings resistant to irreversible Protein adsorption
Products for Capillary Electrophoresis

17. Plastic Chip Design & Fabrication Services
Features
Plastic microfluidic chips
100 micron features
Short turnaround times
Applications
Capillary electrophoresis
Reaction monitoring
Micro-sample prep
Services
Berkely.edu

18. Protein Research Services
Ø BIOiTRAQ capability
Ø Use of our new products, eg TiO2
Ø Gel-based sample capabilities
Ø De Novo Sequencing (PEAKS studio)
Services
www.appliedbiosystems

19. Protein Standards
Products for Solution-Based Proteomics

20. Mark of Quality Assurance

21. Isolate - Fractionate - Collect - Digest - Separate - Analyze
gel protein recovery
protein digestion
protein separation
Disposable micro-cartridges
packed with protein
separation matrices:
hydrophobic
hydrophilic
reverse phase
ion exchange
Connecting Biology to Proteomics