Fortunato T. Dela Peña Secretary
Department of Science and Technology
Danilo L. Concepcion President
University of the Philippines
On behalf of the University of the Philippines, I warmly congratulate the UP Philippine Genome Center (PGC), headed by Executive Director Cynthia Saloma, on the inauguration of its Protein, Proteomics, and Metabolomics Facility (PPMF).
The University celebrates the addition of this critical facility to the UP PGC’s arsenal, which further enables it to fulfill its mission to apply advanced knowledge and emerging technologies in genomics and bioinformatics, health and medicine, agriculture, biodiversity, forensics and ethnicity, industry and the environment for Filipinos’ benefit humanity. With Dr. Neil Andrew Bascos as its Program Director, the PPMF will undoubtedly serve as a venue for collaborative, interdisciplinary work on proteomics and metabolomics research in UP. Through these efforts, UP, the government, and private industry also collaborate further to our country’s quest to fulfill its Sustainable Development Goals, especially in ensuring healthy lives and promoting well-being for all our citizens.
I also thank the Department of Science and Technology, led by Secretary Fortunato de la Peña, for the continuing support for the new facility and the UP PGC itself, especially regarding the state-of-the-art equipment and instruments needed. Thank you for your continued faith in the UP PGC and your commitment to developing the country’s scientific capability, harnessed to serve the Filipino people. Most of all, I thank and congratulate the UP PGC’s scientists, researchers, staff, and partner institutions of the UP PGC on continuing to push the envelope for genomics research and bioinformatics in the country. We in UP look forward to witnessing the new heights of achievement and contribution from the UP PGC in the years to come.
Maraming salamat, at mabuhay kayo!
My warmest congratulations to the team responsible for putting up the Protein, Proteomics, and Metabolomics Facilitly at the Philippine Genome Center (PGC)!
Omics is still a relatively new field but PGC has come a long way from being a pipedream in 2008. It has been more than a decade since the PGC has been conceived and with the opening of the PPM Facility, it continues to evolve into an instituion that could further serve the nation.
PGC’s foray into the world of Omics is an exciting one, especially for us at the Department of Science and Technology (DOST), as it embodies what we envisioned science could do for our countrymen, that of providing solutions tht are tailor-made for Filipino.
The PGC’s growth always stems from the need to respond to the world’s pressing health probelms. From Dengue, to SARS, to H1N1, and now COVID-19, these major health events are a testament to the Center’s enduring relevance, hence, moving forward, we should strive harder to communicate our fellowmen the importance of science in improving their lives.
Now that the bedrocks of our Omics capabilities are laid, we at the DOST are looking forward to witnessing the many feats the PPM Facility and PGC will accomplish in the future. Rest assured that you will have our support in your undertakings.
Thanks to the Metabolomics Facility Team headed by Dr. Neil Andrew Bascos.
Cheers and more power to the Philippine Genome Center!
Maria Cynthia Rose Banzon Bautista, PhD Vice President for Academic Affairs
University of the Philippines
Let me extend a hearty congratulations to PGC Executive Director Cynthia Saloma, the PGC family and Neil Bascos and the PPM Team on this auspicious inauguration of the Protein, Proteomics & Metabolomics Facility, which of course would not have been possible without the DOST Philippine Council for Health Research & Development’s unstinting commitment translated to funding support for the very significant project of laying the infrastructure for the conduct of proteomics and metabolomics studies in the country.
There are at least three fields that are relatively at the frontier in the Philippines for which UP as the country’s national university is expected to develop expertise in, as well as the ability to translate discoveries into innovations and technological solutions to the country’s problems.
These fields are the omics sciences, data science and artificial intelligence. Today’s launching reflects UP’s movement towards fulfilling this expectation for the development of the omics sciences.
Coupled with the DNA Sequencing Core Facility, the equipment and team working in PPM facility will enable PGC to facilitate the development of genomics, proteomics and the newest omics science, metabolomics and yes, bridge the gap in omics research. It is a valuable gift to those of you working in the life sciences. More importantly, however, it will help optimize the university’s contributions to the development of agriculture, health, and forensics.
I am not a natural scientist but what I find exciting are the many possibilities the facility we are inaugurating today will open. For aside from identifying diagnostic markers, proteomics and metabolomics can be used in the discovery of molecules that can be developed into drugs for humans and animals as well as cures for plant diseases. Even more exciting is the possibility of what USEC Montoya referred to as personalized medicine, of developing medicines that are suitable to the genetic make-up of Filipinos and the animals and plants endemic to the country.
Thank you once again to DOST for making the potential contributions of the omics sciences to our people closer to actualization, to Dr Bascos and his team for breathing life to PPMF, and to the PGC family for consistently and painstakingly moving from strength to strength not for itself, not for UP, but for the Filipino people and the advancement of science in general.
Afterall, PGC is in UP and is moved by UP experts, it is merely hosted by UP for the Philippines.
As the PGC mantra goes—PGC para sa Bayan!
My heartfelt congratulations to Dr. Neil Andrew Bascos and his team at the Philippine Genome Center (PGC) on the inauguration of the Protein, Proteomics, and Metabolomics (PPM) Facility.
Finally, the PPM Facility is now open to our researchers and future microbiologists!
I know that the team had high aspirations when they began working on this project and despite the drawbacks brought about by the pandemic, they pressed forward to ensure that the PPM Facility will be fully operational.
Thank you PPMF Team for keeping this dream alive!
The past year has been an eventful one for PGC due to the pandemic. Given the role that PGC plays during this pandemic, we realize the wisdom of DOST’s and UP’s investment in the PGC 8 years ago. We foresee that the PPM Facility that we have just opened to our Filipino scientists and even those in different parts of the globe goes beyond responding to the threat we are now facing.
Many of the microbiology and biotech-based studies of our researchers aim to harness the potential of our natural products as well as recombinant gene expression and protein production techniques to further not just health but also agriculture, forensics, ethnicity, biodiversity, and other industries in our country, be it private or public. With the opening of the PPM Facility, we are now able to provide our scientists with a venue that is conducive for their research. They need not look overseas for protein-based experiment services such as Mass Spectrum analyses because our PPM Facility will have it.
Truly, the PPM Facility heralds exciting times not just for the scientific research community, but for the country in general. This is only the beginning. In the near future, we will be able to provide more locally-available and affordable products and services that would make better the lives of the Filipino people and our economy.
As the PPM Facility project team endeavors to complete its third and final year, I wish everyone at the PGC all the luck and success.
Magandang agham sa ating lahat!
Rowena Cristina L. Guevara, PhD
Undersecretary for Research and Development Department of Science and Technology
Jaime C. Montoya, MD, MSc, PhD, CESO III Executive Director
Philippine Council for Health Research and Development Department of Science and Technology
A decade ago, the UP-Philippine Genome Center was born out of the collaboration of many great Filipino experts and institutions who believe that the field of omics is a game-changer in informing and transforming public health. Today, I am sure all of you will agree that this institution and the field have been significant in countless ways, especially in realizing the goal of personalized medicine, or what we call in PCHRD as “lunas na sakto para sa Pilipino.”
Nowhere is this goal certain without investment, partnerships, and interventions to fuel research breakthroughs that will provide research-based knowledge.
With science at the forefront of our interventions and omics among our arsenal of research methods, I am confident that the goal of personalized medicine is forthcoming. Alongside this mission, we recognize that we need to invest and put in a lot of effort and hard work, including the establishment of facilities and laboratories that will house the many research work and breakthroughs that our scientists are conducting, and are about to do in omics research.
With the opening of the UP PGC’s Protein, Proteomics, and Metabolomics or PPM Facility, I am confident that countless research opportunities and ongoing interventions in omics will come to fruition all for the benefit of the Filipinos. I would like to congratulate the PGC family, our partners, and the stakeholders on this milestone which is hinged on bringing science closer to the Filipino people, and making their lives better through health research. We, at DOST- PCHRD, are proud of those whose contributions have paved the way to finally give rise to the PPM Facility.
Maraming salamat at mabuhay ang UP PGC!
Cynthia P. Saloma, PhD Executive Director
Philippine Genome Center
The opening of the Protein, Proteomics and Metabolomics Facility (PPMF) on 4 October 2021, marks another milestone in the evolving story of the UP Philippine Genome Center. The PPMF is the 3rd PGC core facility to be opened following the opening of the DNA Sequencing Core Facility (DSCF), and the Core Facility for Bioinformatics (CFB). In anticipation of more researches in proteomics and metabolomics, this new facility of the UP PGC is a boon to local scientists who need an array of laboratory services that are otherwise unavailable in their own labs.
Beyond offering laboratory services, training and hands-on workshops, partnerships for research collaborations are among the mechanisms that will be made available to increase and strengthen Omics-research in the country. We are grateful to the Department of Science and Technology, particularly to PCIEERD and PCHRD, for supporting the establishment of the three (3) service facilities at the UP PGC.
The PPMF is yet another avenue for R&D collaboration with clinicians, scientists and students in SUCs, as well as researchers in the private and public R&D organizations. Despite the challenges brought about by the ongoing pandemic brought about by SARS- CoV-2, introducing another facility that makes research in the Philippines incorporate another -omics analysis platform offers renewed hope for many in the science community to continue working on proteomics and metabolomics topics and achieve a deeper analysis of their material in the search for solutions to the various societal problems we face at this time.
#Ang PGC para sa bayan. Mabuhay ang PPMF. Mabuhay ang mga siyentista ng bayan. Mabuhay tayong lahat.
On behalf of the PGC-PPMF staff, I would like to express our heartfelt appreciation for your continued encouragement, guidance, and support as we worked towards the establishment of the first Protein, Proteomics, and Metabolomics Facility in the country.
It has been a long road, paved with vials of blood, buckets of sweat, reams of procurement papers and reports, not just a few tears, and a pandemic.
And, not despite, but through these shared experiences with you, our partners in this quest: officials and staff of the DOST-PCHRD, the UP System, the Philippine Genome Center, Brownstone Asia-Tech, Inc., and other collaborating institutions in the academe, government and industry, we have reached our goal. With you, we are proud to bring forth the country’s most advanced facility for high resolution mass spectrometry analysis.
With this resource, we significantly expand the capacity of Philippine researchers to utilize multi-Omics technologies for relevant research.
Since we began this project, back in 2019, we have been receiving many inquiries and requests from various researchers that would want to employ multi-Omics technology; Proteomics, and Metabolomics in their studies.
Before today, we have had to regretfully state that these types of studies would have to be out-sourced. Sadly, we have had to say “we can’t do this in the Philippines”. Today, things change.
On this day, we officially begin our operations as a fully-functional research and service facility. We gratefully welcome the opportunity and responsibility, to help our fellow researchers in their efforts to improve the lives of our fellow Filipinos, through advancements in the Health, Agricultural, and Industrial sectors.
They say it takes a village. For this huge project, we asked for the help of a Nation. The Filipino people entrusted us with a great resource, and the PGC-PPMF will continuously strive to pay it forward.
In Service of the Filipino People.
Neil Andrew D. Bascos, PhD Program Director
Protein, Proteomics and Metabolomics FacilityUniversity of the Philippines
Mission
Philippine Genome Center
Vision
Goals
The Philippine Genome Center is the country’s leading institution for omics-driven technologies and customized services. We therefore aim to:
To be the premier institution on relevant translational multi-omics research and services in the country that is responsive to the needs of the Filipinos and the society by 2025.
Strategic Plan 2019-2025
train and provide growth opportunities to our scientists, collaborators, and partners while embracing diversity and inclusivity;
commit to the highest level of ethical standards on institutional governance and financial management of allocated resources; and contribute to the macroeconomic growth of the country by continuously seeking new knowledge and innovations in the field of multi-omics sciences
+ + +
SOCIAL RESPONSIBILITY
Position the PGC as an industry leader in big data analytics involving genomics research in the Philippines
GENOMICS APPRECIATION
Increase stakeholders’ recognition and appreciation of genomics OPERATIONAL EFFICIENCY
Ensure operational efficiency as a research unit and service provider SOCIAL ENTREPRENEURSHIP
Explore new business models and maximize existing ones for resource generation and program continuity
LINKAGES
Establish new linkages and maintain collaborations with local and international institutions
SG1
SG2 SG3 SG4
SG5
Time Program 9:00 Ingress
9:15 Philippine National Anthem 9:20 Welcome Remarks
Dr. Cynthia P. Saloma, Executive Director
Philippine Genome Center, University of the Philippines 9:30 Message From UP Diliman Chancellor
Dr. Fidel R. Nemenzo, Chancellor, University of the Philippines Diliman 9:40 PPMF Promotional Video
9:45 Message from DOST Secretary
Hon. Fortunato T. Dela Pena, Secretary, DOST 9:55 Message from DOST Undersecretary for R&D
Dr. Rowena Cristina L. Guevara, Undersecretary, DOST 10:05 Message from DOST-PCHRD Executive Director
Dr. Jaime C. Montoya, Executive Director, DOST-PCHRD 10:15 Message from UP President
Atty. Danilo L. Concepcion, President, University of the Philippines
10:25 Message from UP Vice-President for Academics Affairs
Dr. Maria Cynthia Rose Banzon Bautista, Vice President for Academic Affairs, University of the Philippines
10:35 Unveiling and Ribbon Cutting 10:55 PGC-PPMF Website Launch 11:00
Testimonial Speech
Dr. Doralyn Dalisay, Director, Centre for Chemical Biology and Biotechnology, University of San Agustin
11:10
Closing Remarks
Dr. Neil Andrew D. Bascos, Program Director, PPMF Philippine Genome Center, University of the Philippines
Inauguration of PGC’s Protein, Proteomics, and Metabolomics Facility
Bridging the Gaps of Omics Research
in the Philippines
PGC PPMF
The PPMF will support research programs to uncover functional molecules of biological and biomedical importance.
Complementary to this, PPMF will venture into the discovery and advancement of inventive strategies for the development of various fields and sectors through incorporation of Omics work.
To promote and develop Philippine Omics research, the PPMF will also facilitate the training of researchers all over the country in these relevant technologies. Through this, we hope to share the capacity to utilize Omics technologies with all Filipino scientists.
The PPMF.
Expanding the capabilities for conducting and applying Omics Technology in the Philippines.
In service of the Nation.
PPMF
Establishment
Since 2011, the Philippine Genome Center (PGC) has led the advancement of genomics research in the country. It has provided service to a wide array of sectors such as health, agriculture, and industry and paved the way for the availability of resources and services for genomic studies by Filipino researchers, within the Philippines.
To further expand capabilities for Philippine Omics research, the PGC, with the help of the Department of Science and Technology - Philippine Council for Health Research and Development (DOST-PCHRD), has established the Protein, Proteomics and Metabolomics Facility (PPMF).
The PPMF houses the most high-advanced equipment for proteomic and metabolomic analysis in the Southeast Asian region, as well as other state-of-the-art equipment for the analysis and characterization of protein samples. These resources allow the facility to conduct collaborative research, and perform analytical services for Filipino researchers in the fields of proteomics and metabolomics analysis without the need for out-sourcing.
Protein and proteomic analysis involve the direct assessment of proteins and their expression to gain insight into the different cellular processes occurring in an organism.
Metabolomics focuses on small molecules or metabolites which are metabolic products of physiological processes that also reflect an organism’s condition or state.
The results of these analyses, whether on their own, or in conjunction with genomics research, provide a wealth of information for the understanding of interconnected physiological processes within the subjects under study.
The PPMF represents our country’s investment on the necessary scientific infrastructure and technology platforms to support the health, agriculture, environment, biodiversity, forensics and ethnicity programs of the Philippine scientific community, in service of the Filipino people.
[2] Rayment, I., Protein structure. Encyclopedia of Physical Science and Technology (3rd Edition). (2001) 3rd ed. Elsevier Science.
[3] Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., Baker, D., Improved protein structure prediction using predicted interresidue orientations. Proc. Natl. Acad. Sci. 117, 3 (2020) 1496-1503. DOI: 10.1073/pnas.1914677117 [4] Coskun, O., Separation techniques: chromatography. North Clin. Istanb. 3,2 (2016) 156-160. DOI: 10.14744/
nci.2016.32757
[5] Dimitrov, D.S., Therapeutic proteins. Methods Mol. Bio. 899 (2021) 1-26. DOI: 10.1007/978-1-61779-921-1_1 [6] Agneiray, H., Glasson, J.L., Chen, Q., Kaur, M., Domigan, L.J., Recent developments in sustainably sourced protein-based biomaterials. Biochem. Soc. Trans. 49,2 (2021) 953-964. DOI: 10.1042/BST20200896.
[7] Abascal, N.C., Regan, L., The past, present and future of protein-based materials. Open Biology. 8(10) (2018) 2046-2441.
DOI: 10.1098/rsob.180113.
[8] Murugesan, V., Amarnath, D.J., Bio-process performance, evaluation of enzyme and non-enzyme mediated composting of vegetable market complex waste. Sci. Rep. 10 (2020) 1838. DOI: 10.1038/s41598-020-75766-3
Analytical methods for biomolecules reached new heights with advancements in mass spectrometry (MS) technologies in the early 2000s. In line with the discovery of desoprtion technology (i.e. the successful transfer of macromolecules to ions in the gas phase), scientists were able to utilize MS technologies for the analysis of molecules with increasing complexity. In 2002, the Nobel Prize in Chemistry was awarded to John B. Fenn, Koichi Tanaka (mass spectrometry, MS), and Kurt Wüthrich (nuclear magnetic resonance, NMR), for their game-changing contributions in the field of biomolecular research. Dr. John B. Fenn addressed the challenge of finding a method to weigh something so small, by spraying the sample using a strong electromagnetic field to produce small, charged, freely hovering ions.
Dr. Koichi Tanaka built on this phenomenon further by using an intense laser pulse where molecules would be released as free ions, also called soft laser desorption [1]. These revolutionary breakthroughs led to the rapid and reliable characterization of complex macromolecules in near-native states.
Proteins are a complex class of biomolecules. Composed of amino acids joined by peptide bonds, proteins perform a vast array of biochemical functions depending on their folding patterns, structural organization, and interactions with the environment. Proteins are among the most versatile macromolecules in living systems and are believed to serve crucial functions in essentially all biological processes [2].
Interestingly, the multitude of proteins within cells are composed of the same set of 21 amino acid residues which assemble in a near-infinite number of arrangements, and are then folded three-dimensionally in many different forms.
Their inherent complexity highlights the need to use systematic protocols for their analysis [3]. Chromatographic methods are among the highly-selective techniques employed for this, allowing the deconstruction of a sample material based on their biomolecular properties [4].
Applications of protein characterization research have been used over a wide range of research sectors. In the clinical setting, therapeutic proteins are used as regulators for deficiencies or abnormalities in the biochemical activity of a patient.
Sometimes called “designer proteins”, recombinant proteins are also used to protect against foreign objects, autoimmune diseases, and cancer, in the form of vaccines [5]. Proteins are also frequently used as biomaterial components for biomedical engineering applications. For example, the use of collagen and silk- based proteins - are often incorporated into material composites at the micro and nano-sized scale [6] to improve a biomaterials properties (e.g. elasticity) and compatibility when used in implants [7]. In the agricultural sector, proteins derived from agri-food sources have been used as an additive to increase efficiency in bio- waste processing as well as energy sourcing [8].
Protein characterization has proven to be particularly relevant in light of the current pandemic. Funding has been poured into the characterization of the SARS-CoV-2 spike glycoprotein; responsible for the various immune-responses, and in some cases, lethal effects of the virus.
[1] Tablet, J., Rebuffat, S., Nobel Prize 2002 for chemistry: mass spectrometry and nuclear magnetic resonance. Med. Sci. (Paris) 19, 8-9 (2003) 865-72. DOI: 10.1051/medsci/20031989865.
About Protein Characterization, Proteomics, and Metabolomics
Protein Characterization
Metabolomics research involves the comprehensive identification and classification of metabolites within cells, biofluids, tissues, or organisms. Similar to proteomics, metabolomics aims to investigate the factors involved in the promotion of a target system’s state of function and dysfunction.
Metabolomics-based analyses are typically divided into two categories; global untargeted analysis or targeted analysis. Global untargeted ‘discovery’ analysis allows for the characterization of complex sample analytes with unknown chemical profiles. Discovery of unique factors through these (hypothesis generating) studies may help rationalize the bases for the observed characteristics.
On the other hand, targeted confirmation (i.e. hypothesis validation) analysis involves the quantification of established metabolites in order to determine if the expected changes between tested conditions is actually observable[13].
Analyses of these factors are usually done using mass spectrometry (MS) technologies which can isolate and characterize small molecule metabolites of a given biological sample. Other analytical techniques include the use of the nuclear magnetic resonance (NMR) and Fourier Transform infrared spectrometer (FTIR), which are both rapid and non-destructive methods for metabolite profiling [14].
The field of overlapping omics research is a young, up-and-coming field that has already started to reveal important connections between genomics and systems biology [15]. The continued development of analytical techniques focusing on improving resolution, speed, and increased throughput has steadily supported the growth of the research field [16]. By helping metabolomics and proteomics find its footing in the health, agricultural, and material science sectors of research here in the Philippines, the PPMF hopes to facilitate the promotion of prolific, multi- disciplinary, and productive research in the country.
[13] Clish, C.B., Metabolomics: an emerging but powerful tool for precision medicine. Cold Spring Harb. Mol. Case Stud. 1,1 (2015) a000588. DOI: 10.1101/mcs.a000588
[14] Nalbantoglu, S., Metabolomics: basic principles and strategies. InTech Open (2019). DOI: 10.5772/intechopen.88563.
[15] Mann, S.P., Treit, P.V., Geyer, P.E., Omenn, G.S., Mann, M. Ethical principles, constraints, and opportunities in clinical proteomics. J. MCPro. 20 (2021) 100046. DOI: 10.1016/j.mcpro.2021.100046.
[16] Yates, J.R. III, Recent technical advances in proteomics. F1000Res. 8 (2019). DOI: 10.12688/f1000research.16987.1 [9] Wilkins, M.R., Sanchez, J.C., Gooley, A.A, Appel, R.D., Humphrey-Smith, I., Hochtrasser, D.F., Williams, K.L., Progress with
proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet. Eng.
Rev. 13 (1996) 19-50. DOI: 10.1080/02648725.1996.10647923.
[10] Timp, W., Timp, G., Beyond mass spectrometry, the next step in proteomics. Sci. Adv. 6,2 (2020) eaax8978. DOI: 10.1126/
sciadv.aax8978
[11] Macklin, A., Khan, S., Kislinger, T., Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin. Proteom. 17 (2020). DOI: 10.1186/s12014-020-09283-w.
[12] Aslam, B., Basit, M., Nisar, M.A., Khurshid, M., Rasool, M.H., Proteomics: technologies and their applications. J. Chrom.
Sci. 55,2 (2017) 182-196. DOI: 10.1093/chromsci/bmw167
The term proteome was first coined by Marc Wilkins in 1994 to describe the translated protein complement of a genome [9]. By definition, the proteome is said to make up the component of proteins that is expressed by an organism. Unlike the genome (the set of genes found within an organism), the proteome is not constant and can vary at different locations within an organism. In consequence, references to a proteome are done with respect to a given point in time (i.e., stage in embryonic development or maturation of an organism).
Proteomics is the study of the proteome, exploring the various interactions between proteins and the role of these proteins within the organism. Generally, proteomics studies explore the underlying health- and disease- related biochemical mechanisms at the protein level. Proteomic studies typically require the analysis of several aspects of information regarding the identity, quantification, post- translational modification, localization, functionality, structural, and interactions of the component proteins under study [10].
Several applications of proteomics include the identification of protein markers for diagnostic and prognostic purposes, and the evaluation of a patients’ biochemical response to stem cell therapy, and potentially, the tailoring of disease treatments based on a patient’s unique genetic and epigenetic makeup [11]. Proteomic applications are not limited to clinical research and have shown promising potential in agriculture, food science, system biology, paleoproteomics, and astrobiology [12].
Proteomics Metabolomics
Multi-Omics Research
Cell Lysis
Sample Preparation
Protein Purification (FPLC)
Biomolecule Quantificaition
Facility Services
These methods aim to break down cell membranes for the release and isolation of proteins and metabolites from the specimen for further purification and analysis.
These procedures aim to purify proteins of interest from a crude protein extract. Proteins in solution (e.g. cell lysate) can be separated based on their interactions with different chromatographic columns via the ÄKTA Pure 25 L1 FPLC System.
These methods are for determining the concentrations of biomolecules in samples using colorimetric methods.
These are a selection of miscellaneous processing methods of samples performed prior to purification and analysis.
Sonication (MRC Lab Sonic-250 W)
Disrupt cellular membranes by employing an ultrasonic probe.
Ideal cell solution volume: 10 mL
Ion-Exchange Chromatography
Separate polar molecules according to their charged groups. Target charged proteins may be purified from solution using these types of columns
Bradford Reagent Quantification
Measure the total protein concentration in the sample. This method can detect total protein concentrations of 5-200 μg/mL within a sample Metal Affinity Chromatography
Separate proteins using Ni Sepharose affinity resin columns that allow selective binding of proteins that have a 6X His-Tag
Multiwavelength Spectrophotometer (CLARIOstar PLUS Microplate Reader)
Quantify protein, RNA, and DNA samples with spectrophotometry.
The automated spectrophotometer can process up to 384 samples in a single plate. Available modes in the system are: Absorbance, Fluorescence, and Luminescence Spectroscopy.
Size Exclusion Chromatography
Separate protein mixture components based on their relative sizes.
Columns of different pore sizes are used to target proteins based on their expected molecular weights
Ultracentrifugation (SorvallTM WX 100+)
Fractionate samples based on different densities by spinning samples up to 100,000 rpm or ~800,000 x G
French Pressure Cell
(Glen Mills G-M® High Pressure Cell Disruption)
Employ high-pressure (20,000-40,000 psi) extrusion to disrupt resilient plasma membranes and cell walls of the samples. Ideal cell solution volume: 1-35 mL
Lyophilization (Gyrozen HyperCOOLTM HC3110)
Completely remove the solvent from samples through freeze drying with temperatures up to -110°C
Centrifugal Vacuum Concentration (Gyrozen HyperVACTM) Increase the concentration of samples by removing excess solvent via centrifugation with simultaneous reduction of pressure
Buffer exchange (Amicon® Stirred Cell)
Replace the buffering solvent of the sample through the use of a stirred cell membrane filter which retains solutes of particular molecular weights
Sample Preparation for Proteomics Analysis
Perform reduction-alkylation and proteolytic digestion (e.g. tryptic digestion) on semi-purified and/or purified protein extracts as preparation for further analysis
Protein Characterization
These methods are comprised of different techniques such as polyacrylamide gel electrophoresis (PAGE) for molecular weight determination, western blot analysis for detection of specific molecules, surface plasmon resonance (SPR) analysis for studying the binding kinetics of molecular interactions, and CD-ORD spectroscopy for secondary structure determination.
PGC PPMF
Circular Dichroism (CD) Spectroscopy (Jasco J-1500 CD Spectrometer)
Determine secondary structure, optical isomerism, protein conformation, chiral discrimination, and thermal stability of biomoleculest.
CD-ORD Spectroscopy
High Resolution Mass Spectrometry Western Blot Analysis
SPR Analysis
Polyacrylamide Gel Electrophoresis (PAGE)
This method serves as a preliminary analysis of the protein(s) of interest where the sample is passed through a gel and separated either in its native or linear conformations.
1D PAGE (miniVE Vertical Electrophoresis System)
Separate and quantify protein samples based on molecular weight using an electrophoresis gel.
Molecular Mass Determination of Pure Samples
Determine the accurate monoisotopic mass of your pure protein or metabolite.
CM5 Chip - standard surface
Utilize a chip that is compatible with a broad range of applications such as basic research, quality control, ligand fishing, and fragment-based drug discovery (FBDD). Ligands are covalently coupled via functional groups such as -NH2, -SH, -CHO, -OH, and -COOH.
2D PAGE (EttanTM IPGphorTM 3 IEF System,
SE 600 Ruby Standard Dual Cooled Vertical Electrophoresis Unit) Separate and quantify protein samples first by their isoelectric points and then according to their molecular weights
Optical Rotatory Dispersion (ORD) Spectroscopy (Jasco J-1500 ORDM-520)
Acquire data on chiral molecules even without chromophores by measuring the chirality of non-absorbing samples and checking for absolute configuration.
Putative Identification of Pure Samples via Database Search Compare the pure sample’s mass spectrum against libraries containing mass spectra of thousands of compounds to find the best matches for its putative identity.
De Novo Sequencing of Peptides
Determine the putative identity of peptides from novel or unsequenced sources using de novo sequencing. The peptide will be fragmented via CID, HCD, ETD and/or EThcD.
Protein and Peptide Identification by LC-MS Proteomics
Obtain a proteomic profile of an organism in a given condition. Bottom- up and top-down proteomics can be performed depending on sample condition.
NTA Chip - nitrilotriacetic acid
Perform SPR using a chip designed to bind different types of histidine- tagged molecules such as recombinant proteins via metal chelation.
This chip could be used from low-molecular weight analytes to large proteins.
This analysis detects specific epitopes present in the sample and quantifies the relative amount of the target molecule for protein identification.
This is a biosensor technique that is used in studying binding kinetics and affinity of molecular interactions. Choice between single- or multi-cycle kinetics is possible with the BiacoreTM X100 System.
This analysis is widely used for studying the higher-order structure of biomacromolecules such as proteins, glycoproteins and DNA; subtle changes in the folding of the backbone can be detected in realistic aqueous environments by CD in the far-UV wavelength range.
This powerful method analyzes compounds and biomolecules by fragmenting them into ions that can be detected by the Orbitrap Fusion Tribrid high resolution mass spectrometer. Prior to mass spectrometry, sample components will be separated by liquid chromatography using Vanquish Horizon UHPLC or Ultimate 3000 RSLCNano nanoHPLC.
Automated Trans-Blot (Amersham ECL Semi-Dry Blotter TE 77 PWR Semi-Dry Transfer Unit)
Perform WB using customized membrane blotting protocols or automated standard blotting protocols.
Equipment Use
Personnel Training (available upon request)
Downloadable Forms
Client Information Sheet Order Form I - Protein Services Order Form II - LC-MS Services Client Conforme
Untargeted LC-MS Metabolomics
Perform high-throughput metabolite profiling of a biological sample along with putative identification via database search that could provide a comprehensive insight about the metabolic mechanisms of the specimen
Identification of Post-translational Modifications
Determine the protein’s possible post-translational modifications (PTMs) via software analysis of its mass spectra
Label-free Quantitation
Observe relative changes in amounts of the peptide or metabolite among two varied sets of samples without the need for labeling methods
TMT-Based Quantification for Proteomics
Simultaneously detect and quantify up to 10 samples using isobaric isotope tags such as Tandem Mask Tags (TMT) in a single LC-MS run
PPMF Services focus on the assessment of total protein expression and total metabolite populations in test samples
Equipment
Other Equipment
Multiwavelength Spectrophotometer
Surface Plasmon Resonance (SPR) Spectrometer
Fast Protein Liquid Chromatography
Circular Dichroism (CD) Spectropolarimeter
Ultra-High Performance Liquid Chromatography
High-Resolution Mass Spectrometer
• French Pressure Cell
• Cold Room
• Ultracentrifuge
• Ultrasonic Probe Sonicator
• Large Volume Shaking Incubator
• Lyophilizer
• Centrifugal Vacuum Concentrator
• Stirred Cell Membrane Filter
• 1D PAGE System
• 2D PAGE System
• Western Blot System
• Multipurpose Imaging System
Project Staff Core Staff
Name / Position Degree / School (Year) Neil Andrew D. Bascos, PhDProgram Director
PhD in Molecular and Cellular Biology, Tulane University (2008) Robert Jervine V. Ortega, RCh
University Researcher I
MS Chemistry, University of the Philippines (Ongoing) Manuel Victor B. San Pedro, MSc
Science Research Specialist II
MS Molecular Biology and Biotechnology, University of the Philippines (2019) Maria Patricia H. Diño, RCh
Science Research Specialist II
MS Molecular Medicine, St. Luke’s College of Medicine (Ongoing) Abigail Ruth F. Velasquez, MSc, RCh
Science Research Specialist II
MS Chemistry, University of Santo Tomas (2020)
Mary Stephanie S. Carranza, RCh Science Research Specialist II
BS Biochemistry, De La Salle University (2017)
Owen Tito O. Mallapre Science Research Specialist II
MS Molecular Biology and Biotechnology, University of the Philippines (Ongoing) Patricia Elline O. Palomillo
Science Research Specialist II
Master of Biotechnology, The University of Melbourne (2017) Charles Jason P. Cahilig
Project Assistant II
MS Bioethics, University of the Philippines (Ongoing)
Reichs Daven M. Amar, RMT Laboratory Technician II
BS Medical Technology, Riverside College (2013) Name / Position / Institution Degree / School
(Year) Doralyn S. Dalisay, PhD
Project Staff Level 3
INSTITUTION
University of San Agustin, Iloilo City
PhD in Microbiology, University of New South Wales (2004)
Ricky B. Nellas, PhD Project Staff Level 3
INSTITUTION
Institute of Chemistry, University of the Philippines - Diliman
PhD in Chemistry, Louisiana State University (2010)
Cynthia P. Saloma, PhD Project Staff Level 3
INSTITUTION
Philippine Genome Center
Doctor of Science in Physiology, Osaka University Graduate School of Science (1998)
Baby Rorielyn T. Dimayacyac-Esleta, PhD Project Staff Level 2
INSTITUTION
Institute of Chemistry, University of the Philippines - Diliman
PhD in Chemistry, University of the Philippines - Diliman (2017)
Walter A. Laviña, PhD Project Staff Level 2
INSTITUTION
Institute of Biological Sciences, University of the Philippines - Los Baños
Doctor of Engineering in Biotechnology, Osaka University (2013)
Lilibeth A. Salvador-Reyes, PhD Project Staff Level 2
INSTITUTION
Marine Science Institute, University of the Philippines - Diliman
PhD in
Pharmaceutical Sciences - Medicinal Chemistry, University of Florida (2013) Joel Hassan G. Tolentino, PhD
Project Staff Level 2
INSTITUTION
College of Science and Mathematics, University of the Philippines Mindanao
PhD in Chemistry, University of Connecticut (2008)
FAQs
What services do the PPMF offer?
What is the Modular Analysis Plan (MAP)?
What is the usual service workflow for clients?
The protein, proteomic, and metabolomics facility offers many services geared toward protein analysis, proteomics, and metabolomics. These range from sample preparation, protein purification, protein characterization and quantification, to proteomics and metabolomics analysis using high resolution mass spectrometry.
We invite you to check our website at https://pgc.up.edu.ph/services/ for more details. You may also email us at [email protected] for further discussions on our offered services.
The modular analysis plan is a way for researchers to select a customized workflow.
Through this, clients can mix and match complementary services they wish to avail from the facility to suit their research needs.
The service workflow depends whether the client would like to use the equipment, or to avail sample or data analysis services.
To use the equipment for short term clients or long term*/collaboration:
1. Define the analysis workflow.
2. Confirm sample quality (QC approval) 3. Email PPMF to request a service schedule.
4. Schedule a meeting or consultation with PPMF staff 5. Submit client information sheet and client conforme 6. Provide initial payment
7. Perform experiments
8. Receive Service Report and Billing Statement.
9. Pay remaining balance 10. Receive results from the PPMF
11. Acknowledge receipt of the released data and report
*Long term clients are those who intend to avail the services of the PPMF in the form of a collaborative project.
How do I know if my protein sample is enough for MS Analysis?
How do I send my samples to the facility?
A general marker is if it shows a clear band in a PAGE gel. Alternatively, you may check your protein concentration prior to submission, and consult with the PPMF if this is sufficient for the requested analysis. Some of our procedures require a minimum concentration in order for the service to proceed. For your convenience, the PPMF also offers protein quantification services that you may avail.
Samples should be sent to the following address:
Philippine Genome Center Building
A. Ma. Regidor St., University of the Philippines Diliman, Quezon City 1101
Philippines
We suggest that these be sent through official courier services, and stored accordingly (i.e. with dry ice or ice packs if needed) to prevent sample degradation during transport. Depending on the sample, we may need to perform quality control steps, such as PAGE or quantification, to determine its suitability for analysis. An itemized list of the services conducted for the sample will be provided in the billing statement.
To avail sample or data analysis services:
1. Define the analysis workflow
2. Confirm sample quality (QC approval)
3. Email PPMF to schedule a meeting or consultation with the staff 4. Submit client information sheet and client conforme
5. Provide initial payment 6. Send samples for analysis
7. Receive Service Report and Billing Statement 8. Pay remaining balance
9. Receive results from the PPMF
10. Acknowledge receipt of the released data and report
I want to know something about my protein, but I don’t know what service to avail.
I have picked the services I want to avail from the PPMF?
What is the next step?
My results are bad, how will we go about this?
What times are you open?
How can I track the progress of the service acquired?
We offer consultation services here in the PPMF so that we can provide the best services available. We invite you to check our website at https://pgc.up.edu.ph/
services/ for more details. You may also email us at [email protected] to talk more about our services.
You can request a quotation from us so you can get a budgetary estimate for the service. If you decide to avail our services, we will draft a contract and discuss the terms of the services you have chosen.
Most of our procedures rely on the concentration and the purity of the protein. We suggest checking the quality of your protein through your own means or through other services offered by the PPMF prior to sample analysis. For recombinant protein samples, we strongly suggest the submission of freshly expressed or purified proteins and/or prepared extracts for better results. The ideal time for the best sample quality is within 2 weeks after expression and/or extraction.
Prior to the conduct of analysis experiments, the quality of the test samples will be determined to check their suitability. We will discuss the results of these QC tests with you to help determine the appropriate steps to take before analysis proceeds.
The facility is open Mondays to Fridays from 8:00 am to 5:00 pm except during public holidays. Some experiments may be scheduled to run during the weekends depending on the availability of the equipment.
You may inquire about the status of your sample and/or progress of the service/s through email. An estimated timeline of the analysis will also be provided during the consultation meeting.
How much will the service cost?
How will I receive the report of the analysis or service?
What are the payment terms?
The cost of service will depend on the service/s you would like to acquire. For a quote, please complete a client information sheet or a quote request form.
The client will receive the report and data through email and/or courier service as requested.
Cash/Manager’s Check or Cashier’s Check: Payable to UP System, cash/checks can be delivered to the UP System Cash Office located at the Basement, Quezon Hall Building. Tel. No. 981-8500 local 2618. When using this mode of payment, please bring your FMIS Billing for the issuance of UP System Official Receipt.
*Personal or Company Checks are not accepted.
Bank Deposit Payable to Account Name: UP System Trust Fund – LBP Account No. 1462-1013-64. When using this mode of payment, please send two (2) original validated Deposit Slips to PGC for the issuance of the Bank’s Credit Advice as confirmation of payment.
Transfer of Funds/Voucher Payment: Payable to UP System – PGC Trust Account (Sub Account no. A0004180 for PPMF). This mode of payment is applicable to UP- affiliated clients or government agencies.
When can I submit my samples to the facility?
The PPMF will receive samples from Monday to Friday, 8:00 am to 12:00 nn, and 1:00 pm to 4:30 pm.
PPMF LOCATION
LGF UGF
B 2F 3F P
2nd Flr., PPMF
Philippine Genome Center Bldg.
A. Ma. Regidor Street
University of the Philippines Diliman Quezon City 1101, Philippines
