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Pressure BioSciences, Inc.


PCT MicroTubeTM Adapter Kit*
                                      for
Pressure-Enhanced Enzymatic Proteolysis




   1 hr Trypsin Digest with PCT                     12 hr Trypsin Digest No PCT




     Pressure Cycling Technology
                (PCT)

                   Discovery Starts with Sample PreparationTM



                                  *Patent Pending
Pressure BioSciences, Inc.
                                                       Pressure BioSciences, Inc. (NASDAQ: PBIO) is a life sciences company
                                                       focused on the development and commercialization of a novel, enabling
                                                       platform technology called Pressure Cycling Technology (“PCT”).


                                                                                                   Barocycler
PCT Sample Preparation System
The Pressure Cycling Technology Sample Preparation
System (“PCT SPS”) employs rapid cycles of hydrostatic
pressure, between ambient and ultra high levels, to
precisely control biomolecular interactions. The PCT SPS
can be used to accelerate enzymatic reactions, such as
protein digestion with trypsin and other proteolytic enzymes,
to prepare samples for analysis by mass spectrometry. In
addition, the PCT SPS can be used to disrupt tissues and
cells to extract cellular structures and components such
proteins, lipids, nucleic acids, and small molecules for
further analysis. The PCT SPS is comprised of a Barocycler
(a small, semi-automated bench top instrument used to
generate high, hydrostatic pressure) and specially designed
single-use processing tubes.          Temperature can be
controlled during the PCT-based sample preparation
process by an external circulating water bath, which can be
an important addition to the Pressure Cycling Technology
Sample Preparation System.



  “PCT offers clear advantages over our standard method of sample prep, including shorter processing time,
  higher throughput, and reduced operating costs – and all without sacrificing quality. We found these advantages
  so significant that we recently incorporated PCT into our standard mass spec proteomics analysis workflow.”
  Dr. Shane Burgess
  Director, Life Science and Biotechnology Institute
  Mississippi State University


  PCT MicroTube Adapter Kit*
  Processing time, sample throughput, accuracy, efficiency, and standardization are key elements of the sample preparation
  process for mass spectrometry. The PCT MicroTube Adapter Kit, in combination with the PCT SPS, can reliably and
  reproducibly control the enzymatic digestion of proteins while reducing the time of digestion from hours to minutes with the same
  or better quality as other, currently available techniques. The PCT MicroTube Adapter Kit comes complete with an ergonomically
  designed, space-saving Work Station containing PCT MicroTubes and PCT MicroCaps, as well as tools and hardware, to enable
  the user to process from one to forty eight samples simultaneously in the PCT SPS.

  * Patent Pending


                                                        PCT MicroTube Adapter Kit
PCT MicroTube*
  The PCT MicroTube was designed to meet the critical requirements of modern
  proteomic analysis by mass spectrometry. It is made from a fluoropolymer,
  fluorinated ethylene propylene (FEP). This polymer was selected because of
  its unique features. FEP is highly inert and retains its integrity within an
  extremely wide temperature range (-200oC to +100oC). The PCT MicroTube’s
  outstanding chemical resistance, non-wetting surface, and negligible protein
  and nucleic acid adsorption, help to ensure nearly complete sample recovery,
  features that are essential for high pressure-enhanced enzymatic proteolysis.

  * Patent Pending




                                                             PCT MicroCap*
                                                             PCT MicroCaps were also designed to meet the critical
                                                             requirements of modern proteomic analysis by mass
                                                             spectrometry. They are made from polytetraflouroethylene
           PCT M icroCaps                                    (PTFE), a polymer selected for features that are ideal for
                                                             high pressure applications.          The PCT MicroCap is
                                         Indent for          available in three designs, designated 50, 100, or 150.
                                      Picking G el Plug
                                                             Each MicroCap design designates an approximate reaction
                                                             volume. By selecting a particular MicroCap type, samples
                                                             may be digested in reaction volumes of approximately 50,
                                                             100 and 150 mL. In addition, all PCT MicroCaps have the
100 µ L                                                      added unique feature of being able to be used as gel spot
                                                             pickers to excise and transport small protein spots from a
                            150 µ L                          gel. The PCT MicroCap holds the gel protein spot safely
                                                             within the cap, while it is transferred to the PCT MicroTube,
              50 µ L                                         ready for processing by PCT.

                                                             * Patent Pending




“Incorporating PCT into our standard mass spec workflow has resulted in several significant advantages,
including an improved number of unique peptides identified and a reduction in undesired protein
modifications…and now with the new PCT MicroTube Adapter Kit, throughput will no longer be a bottleneck.”
Dr. Paul Pevsner
New York University School of Medicine




                                             Suggested PCT Workflow
“PCT results in identification of more unique
                                                                         peptides than our standard sample preparation
                                                                         technique for mass spectrometry. It appears that
                                                                         PCT may also be highly successful in digesting and
                                                                         recovery of very complex samples, an area of great
                                                                         difficulty at the present time. These advantages,
                                                                         coupled with the unique characteristics of the
                                                                         recently     designed   PCT    MicroTubes,    offer
                                                                         researchers working in mass spectrometry-based
                                                                         proteomics a wonderful new tool for scientific
                                                                         discovery.”
                                                                         Dr. Alexander R. Ivanov
                                                                         Harvard School of Public Health




Figure 1. Quantitative Profiling of Peptide Abundance for In-Solution
Digested Model Proteins. Selected examples illustrate superior
digestion efficiency and peptide recovery using PCT.
Data provided by Dr. Alexander Ivanov, Harvard School of Public Health




         Figure 2. PCT significantly increases digestion efficiency and peptide recovery following in-solution digestion.
         Digestion was performed using an array of conditions, as indicated. LC-MS was performed on C-18, 10 cm x
         150 µm (VC-10-C18WS-150EU) column using a 30 minute 5-60% gradient (A: 0.1% formic acid; B:
         acetonitrile, 0.1% formic acid) Peptides were detected on an LTQ-Orbitrap XL mass spectrometer with ETD
         ionization source; Alternating ETD/CID spectra were collected and the data were analyzed using Proteome
         discoverer software with 1% FDR data filtering to determine sequence coverage and the total number of
         peptides. Peak areas for selected peptides were measured using LCquan package for each LC/MS run (9
         runs per digest condition). Values were normalized to the average area obtained for each peptide (n=72).
         Median values from each set of 9 LC/MS runs for each peptide and each condition are presented.
         Data provided by Dr. Roger Biringer, Thermo Fischer Scientific
Figure 3. PCT-assisted digestion has been shown to increase efficiency and peptide recovery from
             gel-separated proteins. New consumable containers offer features which facilitate gel spot picking
             using a combination of disposable gel cutter tool combined with the tube closure.
             Data provided by Dr. Michail Alterman, CBER, FDA.




    “We believe that this new patent pending sample containment and processing system, combined with the unique
    power of PCT, gives the researcher extraordinary ability to gain new knowledge using today’s analytical
    identification techniques, such as mass spectrometry. Based on the results from our beta site testers, we believe
    that our PCT MicroTube Adapter Kit can benefit a large segment of the proteomics and genomics research
    community.”
    Dr. Edmund Ting
    Sr. VP of Engineering
    Pressure BioSciences, Inc




      Features and Benefits of the PCT SPS and PCT MicroTubes
       • Standardize Protein Digestion for Mass Spectrometry
       • Substantially Increase Protein Digestion Efficiency
       • Significantly Accelerate In-Solution and In-Gel Protein Digestion
       • Promote Accurate & Efficient Peptide Cleavage
       • Avoid Undesired Protein Modifications Due to Prolonged Digestion Time
       • Process Up to 48 Samples at a Time
       • Versatile Range of Sample Sizes (50-150 µL)
       • Compatible with a Variety of Proteolytic Enzymes
       • Inert, Non-Wetting, Single-Use MicroTube Processing Containers
       • Unique MicroCap Design for Protein Spot Transfer from Acrylamide Gels
.
References

Papers
Schumacher R.T., et al., Automated Solution for Sample Preparation: Nucleic Acid and Protein Extraction from Cells and Tissues Using
Pressure Cycling Technology (PCT). Am. Laboratory. 2002, 34, 38-43

López-Ferrer D, et al., Application of pressurized solvents for ultra fast proteolysis: Proteomics on the fly. J Proteome Res. 2008;7(8).

Gross V., et al., Tissue Fractionation by Hydrostatic Pressure Cycling Technology:
The Unified Sample Preparation Technique for Systems Biology Studies. J Biomol Tech. 2008, 19(3)

Posters
A Comparison of Methods for Efficient Digestion of Protein Therapeutics
Lorna L. Maheu, Heather M. Connelly, Adam G. Harder, and Steven L. Cockrill
Analytical Sciences, Amgen Inc., Longmont, CO 80503
                          th
Poster presented at the 56 ASMS Conference, 2008

High Pressure Trypsin Digestion of Proteins for Proteomic Analysis
Shane A. Wyatt; Timothy R. Croley
Commonwealth of Virginia, Richmond, VA
Poster presented at the 56th ASMS Conference, 2008

Application of Pressurized Solvents for Ultra Fast Proteolysis: Proteomics on the Fly
Daniel Lopez- Ferrer; Konstantinos Petritis; Natacha M Lourette; Brian H. Clowers; Kim K. Hixson; Tyler H Heibeck; Eric A. Livesay; Ryan
Kelly; David Prior; Ljiljana Pasa-tolic; David G. Camp; Mikhail Belov; Richard D. Smith Pacific Northwest National Laboratory, Richland, WA
Poster presented at the 56th ASMS Conference, 2008

IMAGING MALDI of Colorectal Carcinoma-Field Defects in Satellite Tissue
Tiffany Remsen, M. Momeni, P. Kessler, F. Francois, A. Stern, S. Anand, and P. Pevsner
New York University School of Medicine
Poster presented Biomarker World Congress, 2009

Searching for efficient and high-throughput alternatives for essential sample preparation techniques in mass spectrometry-based
functional proteomics
Emily Freeman; Yelena Margolin; Alexander R. Ivanov
Harvard School of Public Health, Boston, MA
Poster presented at the ABRF Conference, 2009

Ultra-Rapid Pressure Digestion and Label-Free Quantitative Proteomics of Yersiniae Infected Mice Tissues
Kim K. Hixson1; Daniel Lopez Ferrer1; Matthew Bender2; Patricia L. Worsham3; Karl K. Weitz1; Nate Lawrence4; Amy Rasley5; Therese W.
Clauss ; Ljiljana Pasa-tolic1; Richard D. Smith1; Mary S. Lipton11Pacific Northwest National Lab, Richland, WA; 2NBACC, Washington, DC;
       1
3
 USAMRIID, Frederick, MD; 4Pressure Biosciences, Inc., South Easton, MA; 5Lawrence Livermore National Lab, Livermore, CA
                            th
Poster presented at the 57 ASMS Conference, 2009

Improved Protein Coverage and Throughput in Proteomics Using On-Line Multiplexed Enzyme Digestions and Targeted MS/MS
with a Modified LTQ-FTICR
Daniel Lopez Ferrer1; Konstantinos Petritis1; Andrei Liyu1; Yufeng Shen1; Benito Canas2; Kim K. Hixson1; Richard D. Smith1; Mikhail Belov1
Poster presented at the 57th ASMS Conference, 2009

Application of pressurized solvents for ultra fast proteolysis: Proteomics on the fly.
1
 PNNL / Battelle Northwest, Richland, WA; 2Universidad Complutense de Madrid, Madrid, Spain
Poster presented at the 57th ASMS Conference, 2009

High-pressure assisted in-gel tryptic digest: qualitative and quantitative aspects
                1                      1                    2               2
Michail Alterman ; Melkamu Getie-Kebtie ; Alexander Lazarev ; Vera S. Gross
1
 FDA, CBER, Rockville, MD; 2Pressure Biosciences, Inc, Woburn, MA;
                          th
Poster presented at the 57 ASMS Conference, 2009

Proteomics under pressure: Rapid extraction and digestion in a single tube
                                2               1               1             1                     2                          th
Alexander Lazarev; Emily Freeman ; Vera S. Gross ; Greta Carlson ; Edmund Ting ; Alexander R. Ivanov Poster presented at the 57
ASMS Conference, 2009


               For more information please visit Pressure BioSciences website: www.pressurebiosciences.com




                                                    For Research Use Only
                                             Not for Use in Diagnostic Procedures

                   Barocycler®, PULSE ®Tubes, PCT MicroTubesTM, PCT MicroCapsTM , ProteoSolveTM
                                            and The PCT Shredder KitTM
                                    are trademarks of Pressure BioSciences, Inc.

                                                                       14 Norfolk Avenue
                                                                       South Easton, MA 02375
                                                                       PH:508-230-1828 Fax:508-230-1829
                                                                       www.pressurebiosciences.com

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PCT MicroTube Adapter Kit for Pressure-Enhanced Enzymatic Proteolysis

  • 1. Pressure BioSciences, Inc. PCT MicroTubeTM Adapter Kit* for Pressure-Enhanced Enzymatic Proteolysis 1 hr Trypsin Digest with PCT 12 hr Trypsin Digest No PCT Pressure Cycling Technology (PCT) Discovery Starts with Sample PreparationTM *Patent Pending
  • 2. Pressure BioSciences, Inc. Pressure BioSciences, Inc. (NASDAQ: PBIO) is a life sciences company focused on the development and commercialization of a novel, enabling platform technology called Pressure Cycling Technology (“PCT”). Barocycler PCT Sample Preparation System The Pressure Cycling Technology Sample Preparation System (“PCT SPS”) employs rapid cycles of hydrostatic pressure, between ambient and ultra high levels, to precisely control biomolecular interactions. The PCT SPS can be used to accelerate enzymatic reactions, such as protein digestion with trypsin and other proteolytic enzymes, to prepare samples for analysis by mass spectrometry. In addition, the PCT SPS can be used to disrupt tissues and cells to extract cellular structures and components such proteins, lipids, nucleic acids, and small molecules for further analysis. The PCT SPS is comprised of a Barocycler (a small, semi-automated bench top instrument used to generate high, hydrostatic pressure) and specially designed single-use processing tubes. Temperature can be controlled during the PCT-based sample preparation process by an external circulating water bath, which can be an important addition to the Pressure Cycling Technology Sample Preparation System. “PCT offers clear advantages over our standard method of sample prep, including shorter processing time, higher throughput, and reduced operating costs – and all without sacrificing quality. We found these advantages so significant that we recently incorporated PCT into our standard mass spec proteomics analysis workflow.” Dr. Shane Burgess Director, Life Science and Biotechnology Institute Mississippi State University PCT MicroTube Adapter Kit* Processing time, sample throughput, accuracy, efficiency, and standardization are key elements of the sample preparation process for mass spectrometry. The PCT MicroTube Adapter Kit, in combination with the PCT SPS, can reliably and reproducibly control the enzymatic digestion of proteins while reducing the time of digestion from hours to minutes with the same or better quality as other, currently available techniques. The PCT MicroTube Adapter Kit comes complete with an ergonomically designed, space-saving Work Station containing PCT MicroTubes and PCT MicroCaps, as well as tools and hardware, to enable the user to process from one to forty eight samples simultaneously in the PCT SPS. * Patent Pending PCT MicroTube Adapter Kit
  • 3. PCT MicroTube* The PCT MicroTube was designed to meet the critical requirements of modern proteomic analysis by mass spectrometry. It is made from a fluoropolymer, fluorinated ethylene propylene (FEP). This polymer was selected because of its unique features. FEP is highly inert and retains its integrity within an extremely wide temperature range (-200oC to +100oC). The PCT MicroTube’s outstanding chemical resistance, non-wetting surface, and negligible protein and nucleic acid adsorption, help to ensure nearly complete sample recovery, features that are essential for high pressure-enhanced enzymatic proteolysis. * Patent Pending PCT MicroCap* PCT MicroCaps were also designed to meet the critical requirements of modern proteomic analysis by mass spectrometry. They are made from polytetraflouroethylene PCT M icroCaps (PTFE), a polymer selected for features that are ideal for high pressure applications. The PCT MicroCap is Indent for available in three designs, designated 50, 100, or 150. Picking G el Plug Each MicroCap design designates an approximate reaction volume. By selecting a particular MicroCap type, samples may be digested in reaction volumes of approximately 50, 100 and 150 mL. In addition, all PCT MicroCaps have the 100 µ L added unique feature of being able to be used as gel spot pickers to excise and transport small protein spots from a 150 µ L gel. The PCT MicroCap holds the gel protein spot safely within the cap, while it is transferred to the PCT MicroTube, 50 µ L ready for processing by PCT. * Patent Pending “Incorporating PCT into our standard mass spec workflow has resulted in several significant advantages, including an improved number of unique peptides identified and a reduction in undesired protein modifications…and now with the new PCT MicroTube Adapter Kit, throughput will no longer be a bottleneck.” Dr. Paul Pevsner New York University School of Medicine Suggested PCT Workflow
  • 4. “PCT results in identification of more unique peptides than our standard sample preparation technique for mass spectrometry. It appears that PCT may also be highly successful in digesting and recovery of very complex samples, an area of great difficulty at the present time. These advantages, coupled with the unique characteristics of the recently designed PCT MicroTubes, offer researchers working in mass spectrometry-based proteomics a wonderful new tool for scientific discovery.” Dr. Alexander R. Ivanov Harvard School of Public Health Figure 1. Quantitative Profiling of Peptide Abundance for In-Solution Digested Model Proteins. Selected examples illustrate superior digestion efficiency and peptide recovery using PCT. Data provided by Dr. Alexander Ivanov, Harvard School of Public Health Figure 2. PCT significantly increases digestion efficiency and peptide recovery following in-solution digestion. Digestion was performed using an array of conditions, as indicated. LC-MS was performed on C-18, 10 cm x 150 µm (VC-10-C18WS-150EU) column using a 30 minute 5-60% gradient (A: 0.1% formic acid; B: acetonitrile, 0.1% formic acid) Peptides were detected on an LTQ-Orbitrap XL mass spectrometer with ETD ionization source; Alternating ETD/CID spectra were collected and the data were analyzed using Proteome discoverer software with 1% FDR data filtering to determine sequence coverage and the total number of peptides. Peak areas for selected peptides were measured using LCquan package for each LC/MS run (9 runs per digest condition). Values were normalized to the average area obtained for each peptide (n=72). Median values from each set of 9 LC/MS runs for each peptide and each condition are presented. Data provided by Dr. Roger Biringer, Thermo Fischer Scientific
  • 5. Figure 3. PCT-assisted digestion has been shown to increase efficiency and peptide recovery from gel-separated proteins. New consumable containers offer features which facilitate gel spot picking using a combination of disposable gel cutter tool combined with the tube closure. Data provided by Dr. Michail Alterman, CBER, FDA. “We believe that this new patent pending sample containment and processing system, combined with the unique power of PCT, gives the researcher extraordinary ability to gain new knowledge using today’s analytical identification techniques, such as mass spectrometry. Based on the results from our beta site testers, we believe that our PCT MicroTube Adapter Kit can benefit a large segment of the proteomics and genomics research community.” Dr. Edmund Ting Sr. VP of Engineering Pressure BioSciences, Inc Features and Benefits of the PCT SPS and PCT MicroTubes • Standardize Protein Digestion for Mass Spectrometry • Substantially Increase Protein Digestion Efficiency • Significantly Accelerate In-Solution and In-Gel Protein Digestion • Promote Accurate & Efficient Peptide Cleavage • Avoid Undesired Protein Modifications Due to Prolonged Digestion Time • Process Up to 48 Samples at a Time • Versatile Range of Sample Sizes (50-150 µL) • Compatible with a Variety of Proteolytic Enzymes • Inert, Non-Wetting, Single-Use MicroTube Processing Containers • Unique MicroCap Design for Protein Spot Transfer from Acrylamide Gels .
  • 6. References Papers Schumacher R.T., et al., Automated Solution for Sample Preparation: Nucleic Acid and Protein Extraction from Cells and Tissues Using Pressure Cycling Technology (PCT). Am. Laboratory. 2002, 34, 38-43 López-Ferrer D, et al., Application of pressurized solvents for ultra fast proteolysis: Proteomics on the fly. J Proteome Res. 2008;7(8). Gross V., et al., Tissue Fractionation by Hydrostatic Pressure Cycling Technology: The Unified Sample Preparation Technique for Systems Biology Studies. J Biomol Tech. 2008, 19(3) Posters A Comparison of Methods for Efficient Digestion of Protein Therapeutics Lorna L. Maheu, Heather M. Connelly, Adam G. Harder, and Steven L. Cockrill Analytical Sciences, Amgen Inc., Longmont, CO 80503 th Poster presented at the 56 ASMS Conference, 2008 High Pressure Trypsin Digestion of Proteins for Proteomic Analysis Shane A. Wyatt; Timothy R. Croley Commonwealth of Virginia, Richmond, VA Poster presented at the 56th ASMS Conference, 2008 Application of Pressurized Solvents for Ultra Fast Proteolysis: Proteomics on the Fly Daniel Lopez- Ferrer; Konstantinos Petritis; Natacha M Lourette; Brian H. Clowers; Kim K. Hixson; Tyler H Heibeck; Eric A. Livesay; Ryan Kelly; David Prior; Ljiljana Pasa-tolic; David G. Camp; Mikhail Belov; Richard D. Smith Pacific Northwest National Laboratory, Richland, WA Poster presented at the 56th ASMS Conference, 2008 IMAGING MALDI of Colorectal Carcinoma-Field Defects in Satellite Tissue Tiffany Remsen, M. Momeni, P. Kessler, F. Francois, A. Stern, S. Anand, and P. Pevsner New York University School of Medicine Poster presented Biomarker World Congress, 2009 Searching for efficient and high-throughput alternatives for essential sample preparation techniques in mass spectrometry-based functional proteomics Emily Freeman; Yelena Margolin; Alexander R. Ivanov Harvard School of Public Health, Boston, MA Poster presented at the ABRF Conference, 2009 Ultra-Rapid Pressure Digestion and Label-Free Quantitative Proteomics of Yersiniae Infected Mice Tissues Kim K. Hixson1; Daniel Lopez Ferrer1; Matthew Bender2; Patricia L. Worsham3; Karl K. Weitz1; Nate Lawrence4; Amy Rasley5; Therese W. Clauss ; Ljiljana Pasa-tolic1; Richard D. Smith1; Mary S. Lipton11Pacific Northwest National Lab, Richland, WA; 2NBACC, Washington, DC; 1 3 USAMRIID, Frederick, MD; 4Pressure Biosciences, Inc., South Easton, MA; 5Lawrence Livermore National Lab, Livermore, CA th Poster presented at the 57 ASMS Conference, 2009 Improved Protein Coverage and Throughput in Proteomics Using On-Line Multiplexed Enzyme Digestions and Targeted MS/MS with a Modified LTQ-FTICR Daniel Lopez Ferrer1; Konstantinos Petritis1; Andrei Liyu1; Yufeng Shen1; Benito Canas2; Kim K. Hixson1; Richard D. Smith1; Mikhail Belov1 Poster presented at the 57th ASMS Conference, 2009 Application of pressurized solvents for ultra fast proteolysis: Proteomics on the fly. 1 PNNL / Battelle Northwest, Richland, WA; 2Universidad Complutense de Madrid, Madrid, Spain Poster presented at the 57th ASMS Conference, 2009 High-pressure assisted in-gel tryptic digest: qualitative and quantitative aspects 1 1 2 2 Michail Alterman ; Melkamu Getie-Kebtie ; Alexander Lazarev ; Vera S. Gross 1 FDA, CBER, Rockville, MD; 2Pressure Biosciences, Inc, Woburn, MA; th Poster presented at the 57 ASMS Conference, 2009 Proteomics under pressure: Rapid extraction and digestion in a single tube 2 1 1 1 2 th Alexander Lazarev; Emily Freeman ; Vera S. Gross ; Greta Carlson ; Edmund Ting ; Alexander R. Ivanov Poster presented at the 57 ASMS Conference, 2009 For more information please visit Pressure BioSciences website: www.pressurebiosciences.com For Research Use Only Not for Use in Diagnostic Procedures Barocycler®, PULSE ®Tubes, PCT MicroTubesTM, PCT MicroCapsTM , ProteoSolveTM and The PCT Shredder KitTM are trademarks of Pressure BioSciences, Inc. 14 Norfolk Avenue South Easton, MA 02375 PH:508-230-1828 Fax:508-230-1829 www.pressurebiosciences.com