Proposal

Introduction

Proposal ID 2015-045
Submitted January 16, 2015
Owner TruxalCarlson
Department Oceanography, School of
Category Machinery & Research
Funding Status Fully Funded
Metric Score 4.16

Contacts

Primary
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Laura Truxal Carlson
  • Research Scientist
  • truxal@uw.edu
  • 206-221-6732
  • UW Box 357940
Budget
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Maura Murphy
  • Grant and Contract Coordinator
  • maurapm@uw.edu
  • 206-543-5188
  • UW Box 357940
Dean
  • Name
  • Title
  • Email
  • Phone
  • Mailbox
  • Lisa Graumlich
  • Dean of College of the Environment
  • envdean@uw.edu
  • 206-221-0908
  • UW Box 355355

Descriptions

Abstract

The majority of life on earth can only be seen with the aid of a microscope. Despite this fact, microorganisms produce half the oxygen we breathe, control the composition of carbon dioxide and other gases in the atmosphere, are important sources for new medicines and biofuels, and form the base of the entire marine food web. Greater knowledge of microbial metabolism, activity and interactions in the environment is essential. A team of investigators who are users of the Marine Microbial Research Center (MMRC), housed and maintained in the School of Oceanography, is requesting equipment to aid in the preparation of samples to facilitate investigations of the unique metabolic capability of environmentally relevant microorganisms. Both graduate students and undergraduate students are the main users of the MMRC and through the acquisition of this equipment they will have access to training in cutting edge approaches that will prepare them for a wide variety of opportunities.

Category Justification

The requested items are for scientific inquiry and research development. Fast track funding is requested to enable the immediate acquisition of equipment that is needed for current student projects and to ensure that it is installed in time for undergraduate senior thesis proposals for the 2015-2016 academic year.

Background

The genomic revolution has opened our eyes to the vast world of microorganisms all around us. In order to more fully characterize the unique capabilities of microbes and their role in the sustainability of our planet, we now use post genomic methods such as proteomics (analysis of proteins) and metabolomics (analysis of small molecules involved in metabolism). The MMRC was founded in 2013 to establish a facility for the application of cutting-edge instrumentation and methods toward research on environmental microbes. We are now equipped with two state-of-the-art liquid chromatography-mass spectrometers (LC-MSs) that can detect and identify hundreds of small molecule metabolites and proteins, even those that are among the most rare. This instrumentation, generally only available in biochemical and pharmaceutical research, allows us to investigate the metabolism and activity of microorganisms in cultures and in the environment. Users of the MMRC are interested in biogeochemical consequences of the activity of microbes, interaction among microbes (phytoplankton, bacteria and archaea), stress responses of microorganisms, and development of microbe-based biofuels. Cultures of these microbes are maintained in labs of users of the facility, field samples are routinely collected, and experiments on how these organisms interact and respond to environmental stress such as nutrient limitation and temperature are already underway. The high-resolution mass spectrometers in the MMRC are used for targeted analyses of key primary and secondary metabolites as well as proteins that make up biosynthetic pathways that translate these microbial interactions and indicate stress.

The acquisition of instrumentation housed in the MMRC facility has necessitated the development of new sample preparation protocols to match the new analytical techniques that accompany our new instrumental capability. While the MMRC is now among the most state-of-the-art analytical facilities in the country focused on environmental microbes, we are lacking the necessary equipment to conduct routine sample processing. The mission of the MMRC is to be an open facility that serves the community of student users by providing expert mentoring and facilities to aid in their studies of environmental microbes. The MMRC can only fulfill this mission if it can offer students facilities and expertise in processing samples so that they are properly prepared for analysis on the MMRC mass spectrometers. Sample preparation requirements for proteomics and metabolomics are extremely sensitive and extractions involve keeping samples cold, in the dark, and protected from risk of contamination. Sample processing and analysis need to be done quickly under controlled and reproducible conditions with sample analysis sometimes needing to happen within hours of sample preparation. This is not currently possible due to lack of accessible equipment. This is a problem for all users, but is a particularly large obstacle for graduate students and undergraduates who come from labs outside of the Ocean Sciences Building (where the MMRC is housed) who want to use these tools, but may not have access to facilities or expertise necessary to prepare samples in their home labs. Some (but not most) of the equipment needed for sample preparation exists nearby (a balance and a centrifuge), but is located in a restricted radiocarbon clean zone that is not accessible to students or samples coming into our building that have been in other labs around campus. The original Major Research Instrumentation award that funded the MMRC only allowed funding for purchase of the primary equipment, the mass spectrometers.

Only in its second year of existence, and first year of operation, the MMRC already hosts students from labs in Civil and Environmental Engineering, Chemical Engineering, Microbiology, Biological Oceanography and Chemical Oceanography. We hope to expand the number of collaborators we have and ensure that we are providing high quality data, but this will not be possible unless we can have a totally open facility with uniform protocols for sample preparation and proper mentoring of student users in how samples need be prepared. Having sample preparation facilities on site that are accessible to all and are housed in a single lab will allow us to ensure access for any interested student, reproducible sample handling and ultimately, high quality data.

Benefits to Students and the University

Students from several departments across campus are already benefiting from the instrumentation in the MMRC. In its first two years of operation we have carried out projects with six graduate students, five undergraduate students, and three postdocs from the labs of five faculty members. With a fully capable and accessible lab, we believe this number will grow rapidly to a standing stock of 20-30 direct users each year, with most of this growth coming from undergraduates. A unique feature of the School of Oceanography is its two research ships stationed at the UW port on the ship canal. UW students, both graduate and undergraduate, travel many thousands of miles on these vessels each year throughout Puget Sound and around the world doing both on-ship analyses and collecting water samples for analysis in their labs on campus. Even more unique is the inclusion of a “senior cruise” in the undergraduate curriculum where each senior in the School of Oceanography designs an original research project and carries it out on board a two-week cruise. The requested instrumentation would give undergraduate and graduate students an expanded arsenal of analytical techniques to design their projects around. Completion of thesis projects in the MMRC will prepare students for jobs in a number of industries (government and environmental consulting) and graduate school in a variety of fields. Working in the MMRC is excellent preparation for these opportunities.

Metabolomics and proteomics are areas of research that have not been widely applied to marine microorganisms or the environmental sciences more generally. This instrumentation will allow undergraduate students in the School of Oceanography to write their senior theses and graduate students to write their PhD dissertations using innovative technology and research that will greatly advance our knowledge in the fields of oceanography, microbial ecology, biotechnology and on the impact humans have on natural ecosystems. Likewise, other MMRC users from across campus will have full access to a facility that they can use to process and analyze their samples in a single lab under the supervision of skilled experts, ensuring data quality.

An important consideration when assessing the benefit of the requested instrumentation is the relatively long lifetime of such equipment. Unlike computer software or hardware that is typically obsolete in 3-5 years, the projected lifetime of well-maintained scientific instruments is on the order of 10-15 years. The requested instrumentation can be expected to continue serving students for many years.

Departmental Endorsements

As a researcher who uses the MMRC (Microbial Metabolomics Research Center) and frequently mentors undergraduate and graduate students, I offer my full support of this proposal. The MMRC is equipped with cutting-edge analytical instrumentation, and the acquisition of the appropriate sample preparation tools would allow for streamlined processing of samples, and would make the center more accessible to students from all over campus. Some of the sample prep steps needed to run samples on our MMRC instrumentation require the use of tools that are in our restricted, radio-carbon clean lab (balances and centrifuge), other tools are not present in our building at all (all other requested equipment). The rules of the restricted lab prohibit the entrance of people and samples that have been in other science buildings on campus. When mentoring students, this is an issue because any person who wishes to enter the restricted area must not have been in any other science buildings, or they must shower and change their clothing, prior to their entering the restricted area. Many of the students wishing to work in our labs have classes that require them to be in other science buildings throughout the day, so finding a time when they can enter the restricted lab is a challenge, and often requires the restructuring and redesign of student projects. Having the appropriate tools in the MMRC would allow for all steps of the preparation of samples to happen outside of the restricted area, thus increasing the accessibility of our state-of-the-art instrumentation to students.

Jaqui Neibauer, Research Scientist, School of Oceanography

I wanted to clearly express how important I think the Student Technology Fund request is that you are composing. Yesterday I conducted a phone interview with a well-respected analytical chemist who is filling an opening at WA-DOE. He is considering a recent graduate who, through her work in a lab, has gained considerable technical skill. He said that the skills she gained at UW placed her well above the other applicants. This is a great example of the unique things a research-1 university can offer an undergraduate. Your request for sample processing equipment will make the MMRC available to many undergraduate and graduate students. This is nothing but good.

Rick Keil, Professor, School of Oceanography

I strongly support this STF proposal to acquire equipment that would allow for uniform processing of samples for the MMRC. My research is focused on understanding the ecology and physiology of microorganisms in the ocean. Marine microbial ecology is a growing field with relevance to the habitability of our planet and sustainability of human societies. My group is engaged in proteomic and metabolomics analyses that aim to uncover the interactions among microbes in the ocean. The methods that we develop will help further our own research, but more importantly, our approach is to share our protocols with any student wanting to use our methods in their own research. Given the potential for widespread adoption of our methods, it is imperative that we be able to provide access to the most widely accepted protocols that will allow students to process samples with the efficiency and care that is required to ensure data reproducibility. Undergraduates working in the MMRC have a particularly hard time given that part of my lab resides in a restricted zone. While we have a balance and a centrifuge in a nearby lab, this equipment cannot be used to prepare samples that have been partially processed in the MMRC. This is because samples cannot reenter the restricted radiocarbon free zone without sample handling that would compromise the quality of the data we generate. The rest of the equipment requested is not present in the Ocean Sciences Building. We have been limping along with the facilities we have and making due while we test methods and set up protocols, but it is essential to the success of current and future MMRC student users that we be able to provide complete facilities for sample handling. The MMRC is among a handful of labs of its kind that focuses on environmentally relevant microorganisms. However, the techniques that are used in the MMRC are widely employed across many fields of research. These approaches demand high quality facilities that can be overseen by trained lab technicians, like those currently working in the MMRC. The training students will receive from these technicians will allow them to complete their research while at UW, but will also better prepare them for the job market.

Anitra Ingalls, Associate Professor, School of Oceanography, Director of the Microbial Metabolomics Research Center

I am strongly supportive of this proposal to help work on microbial metabolomics. I work on the cycling of one-carbon compounds, which are all greenhouse gases, in the natural environment. We track microbial metabolism of these compounds in communities by 13C-flux labeling and by analyzing metabolic pools. For this work, both my undergraduate and graduate students require access to the Microbial Metabolomics Research Center instruments. However, at this time, they must prepare samples in our laboratory and transport them across campus to the laboratory containing the instrument. Having a sample preparation facility will ensure highly reproducible data, which is always an issue with these types of experiments. In addition, it will enable a set of experiments we would like to carry out that are not currently possible due to the need to analyze the samples immediately after their preparation and also due to the restriction of samples that have been prepared in a building in which 14C samples have ever been utilized. At any one time I usually have three graduate students and 3-6 undergraduate students involved in this research.

Mary E. Lidstrom, Professor of Microbiology and Chemical Engineering
University of Washington Vice Provost for Research

I strongly support this Student Technology Fund proposal. My research uses genome-based approaches to analyze microbial interactions in the sea. Today, proteomics and metabolomics of microbes generated both from laboratory experiments and from field studies are increasingly important to better understand microbial interactions. Currently, one postdoc, two graduate students, and an undergraduate from my group are actively engaged in collaborations with researchers from the Microbial Metabolomics Research Center (MMRC) and I expect this number to grow. My lab is located in Ben Hall and we do not have the expertise or facilities to prepare samples for analyses. Furthermore, my personnel and samples are restricted from entering the specialized 14C-free lab within the Ocean Sciences Building where many of the needed facilities reside. My students would greatly benefit from having access to a sample preparation facility where they can also learn proper sample handling techniques. The requested equipment would minimize issues related to sample handling by allowing my students to work closely with MMRC staff and prepare samples in a standardized manner. This approach would allow student training in the best lab practices and would enhance data reproducibility.

Ginger Armbrust, Director and Professor, School of Oceanography

I fully support this request for STF funds. My research involves using organic compounds and their isotopes to reconstruct past climate, particularly in the tropics. In our work, my group uses radiocarbon to date climate events in the past. We also grow cultures of model organisms to understand and calibrate our climate proxies. In these studies, proteomics and metabolomics can provide invaluable insights into the workings of our proxies. My students require a space that is absolutely sure to remain radiocarbon clean for dating samples and also have interest in pursuing research that might entail use of the MMRC instrumentation. Thus, the acquisition of the requested equipment would serve my students by aiding in the maintenance of our radiocarbon clean space and by providing them research tools to pursue their research involving microbial metabolism and how it relates to climate.

Julian Sachs, Professor, School of Oceanography

This letter confirms my enthusiastic support for your STF proposal. The Microbial Metabolomics Research Center (MMRC) has quickly developed into an essential service for the University of Washington research community. The equipment acquired through the STF would be a wonderful mechanism to enhance the MMRC’s capability, making it even more attractive to our research community. My research group would certainly take advantage of this enhanced center capability. In particular, my research relating the physiology of environmental microorganisms to system level processes would clearly benefit from the requested sample preparation addition to the MMRC - proteomic and metabolomic analyses are increasingly recognized as essential methods (complementing genetic surveys) to link micro-scale and macro-scale processes. It essential that our students (both undergraduate and graduate) acquire these skills, as is best accomplished through experience. Having an accessible sample preparation facility attached to the MMRC would therefore be an ideal vehicle to enable student training in skills essential to research in the environmental sciences. I fully agree this is a much-needed addition to the MMRC and I am in complete support of your proposal.

Dave Stahl, Professor, Civil and Environmental Engineering

I am a postdoctoral researcher in the lab of Prof. Anitra Ingalls working within the Microbial Metabolomics Research Center (MMRC). Our laboratory and the MMRC would greatly benefit from the purchase of these instruments, which would help to support our proteomic and metabolomic research projects. These instruments would allow us to streamline our current proteomic and metabolic sample preparation techniques, enabling us to provide efficient and accurate sample analyses throughout our experiments. In addition, this instrumentation will provide us with the tools we need to develop novel methods and sample preparation techniques within our research projects. I strongly support this proposed instrumentation funding.

Rachel A. Lundeen, Postdoctoral Research Associate, School of Oceanography

Installation Timeline

The instruments and equipment will be ordered immediately upon the award of funds and will be installed as soon as delivered. Since all of the requested equipment is typically in stock from US distributors, we expect all requested items to be available for student use within one month of funding.

Resources Provided by Department

Technicians within the Chemical Oceanography curricular group in the School of Oceanography will be responsible for installing, maintaining, and scheduling user-time on the instruments. The Chemical Oceanography group employs six full time oceanographers and analytical chemists to oversee lab facilities, train students on proper use and upkeep of instruments, and to assist student researchers in collecting data and interpreting results. The MMRC and Oceanography facilities currently operate and maintain a broad spectrum of analytical instrumentation, including mass spectrometers, gas chromatographs, high-performance liquid chromatography systems, spectroscopic isotope analyzers, as well as numerous smaller instruments. Necessary infrastructure including power distribution, compressed gas distribution, and ultrapure water supply are already in place in the MMRC and Ocean Sciences Building.

Access Restrictions (if any)

The requested instruments will be installed in the MMRC lab that is a shared instrument facility in the Ocean Sciences Building. Access will be granted to any UW researcher, graduate or undergraduate, with a demonstrated need for the instruments, as well as for coursework that could benefit from them. The requested instrumentation is fairly easy to use and can be operated by anyone after some initial training from staff in the MMRC lab. Once trained, students can be granted building and lab access for experiments that proceed on timeframes outside of normal working hours.

Student Endorsements

The Microbial Metabolomics Research Center has outstanding analytical capabilities with the potential to address research topics from a wide variety of fields. As a chemical oceanography student I use this facility in my research and know first-hand that we are currently limited by our ability to efficiently process samples. The equipment being purchased by this grant would greatly improve and expedite the sample preparation procedure, allowing us to more fully realize the capabilities of the MMRC. This equipment would not only benefit students in oceanography but anyone who might want to use the center for their research. I strongly support this proposal and think it would be a wise use of student technology funding.

Angie Boysen, Graduate Student, School of Oceanography

As an undergraduate student I would like to extend my support for new instrumentation in the Microbial Metabolomics Research Center, as it would improve the overall efficiency and expand the skills of the laboratory. Although I have just recently started working in the lab, learning procedures with the new instrumentation will be beneficial for any future experiments and in my future research career. Additionally, since it would be obtained through student funds it would be available to any other students wishing to conduct an experiment which would be a positive change for the research community at the University of Washington.

Alexandra Wied, Undergraduate Student, School of Oceanography

As a graduate student in Chemical Oceanography at the University of Washington, some of the most important aspects of my PhD research occur within the Microbial Metabolomics Research Center (MMRC). Although the existing MS instrumentation is impressive and state-of-the-art, the related instrumentation and equipment needed to do sample preparation can be lacking. In order for the MMRC to develop into a world-class analytical lab and user facility, we will need to invest in high quality, reliable sample-prep equipment. Graduate and undergraduate students will be able to use these instruments to further our skill sets and conduct our independent research. Through support from the Student Technology Fee Committee, the MMRC will have both MS instrumentation that is available through the user facility, but also the proper equipment for sample preparation and processing.

Katherine Heal, Graduate Student, School of Oceanography

I am a graduate student working with Prof. Armbrust in the School of Oceanography. We would greatly benefit from access to a space to prepare and run mass spec samples that is outside the C14 restricted zone. Our lab is located in a building that is not C14 restricted and therefore to use any equipment in the C14 zone in Ocean Sciences Building I would have to shower upon each visit and buy a special set of clothes for entering the C14 zone. We would like to investigate the metabolite profile of our model diatom using the mass spec facilities in collaboration with the Ingalls lab, but slow sample prep due to C14 zone restrictions will greatly hinder our progress.

Gwenn Hennon, Graduate Student, School of Oceanography

I am a graduate student in Chemical Oceanography. The ability to do efficient sample preparation for metabolite and protein analysis would benefit my work and the work of many of my fellow scientists in oceanography. If these resources were available to me, I would be able to investigate organism-environment interactions in my study location - the marine lakes of Palau. Having this instrumentation outside of the C14-restricted zone would greatly increase accessibility as well as productivity.

Tessa McGee, Graduate Student, School of Oceanography

I am a graduate student in Chemical Oceanography, and my research involves measuring isotope ratios in mangrove and algal lipids for use as paleoproxies. Access to a sample preparation set up outside of the C14 restricted zone would be very useful because the mangrove samples that I collect do not need to be processed in the restricted zone. It would be much easier and less risky to process these samples outside of the restricted zone, for instance when I need to do solid phase extraction. In addition, if there was a set up to efficiently prep my samples for protein analysis, I could potentially analyze specific protein abundances in my mangrove leaf samples, which would help me further understand the biochemical mechanisms of photosynthesis and lipid production in mangroves.

Marta Wolfshorndi, Graduate Student, School of Oceanography

I fully support this request for funding for additional sample preparation equipment for the mass spec lab in Oceanography. Currently, much of this equipment is spread across several labs in the C14-clean zone in Oceanography. This adds an extra level of complexity when preparing samples, especially when training undergraduates in lab research. Having all sample preparation equipment in one place will greatly increase the amount of work that we can get done and the ease with which we can bring undergraduates into our research.

Will Gagne-Maynard, Graduate Student, School of Oceanography

I am a graduate student in the Biological Oceanography department and I collaborate with Anitra Ingalls’ lab. The building I work in is not a C14 restricted zone so I am not allowed to enter the clean zone in the Ingalls’ lab. I want to be involved in preparing metabolite samples at some point in the future, however the necessary equipment is located in the clean zone. If the student technology fee funded this proposal for extra equipment located outside of the clean zone, then this would accelerate the pace of my research and foster interdisciplinary collaboration.

Helena van Tol, Graduate Student, School of Oceanography

As an undergraduate research assistant for UW River Systems Research Group, the requested funds would enable me greater ease of access to instruments which are vital to my research. Currently, the majority of my work is completed within the Carbon 14 decontaminated lab; this lab is designated as such to ensure accurate isotopic analysis without fear of contamination from outside sources. However, this restricted lab zone means that I cannot traverse between other science buildings, such as the chemistry or physics buildings, without showering and completely changing my clothes. This results in restricting my access to the lab and to completing my necessary procedures. The funds awarded would be used to purchase instruments for the contaminated lab and enable increased efficiency of our research. It would also increase the opportunity for undergraduates to get involved in our research by enabling research outside of the decontaminated lab.

Rebekka Gould, Undergraduate Student, School of Oceanography

I am a second-year student in chemical oceanography. My research primarily focuses on the Mg/Ca paleoproxy in foraminifera. I would be interested in doing proteomics work in my research, and the equipment proposed would allow me to prepare my samples so I can take my research in this new and interesting direction. Because of that, I support the request to purchase this equipment.

Elisa Bonnin, Graduate Student, School of Oceanography

As a senior oceanography major, I had the great fortune of being able to plan and execute nearly any senior project that I desired. The only limitations on senior projects are scientific relevance and the equipment available on campus to perform the proposed experiments. The proposed equipment will allow future senior undergraduates to propose projects using proteomic and metabolomic techniques, with hands-on access to state-of-the art equipment not currently available to students. I fully support this proposal.

Colton Skavicus, Undergraduate Student, School of Oceanography

I am a PhD candidate in Chemical Oceanography. I am interested in understanding how phytoplankton cells respond to different environmental conditions. One way to study cellular changes is to grow organisms in a range of different conditions and examine their protein and small metabolite composition. My research would directly benefit from this equipment because my current sampling strategy is hindered by the rules of the 14C restricted clean zone in my building. Having access to this equipment outside the 14C restricted zone will not only save time during sampling but will also improve sample quality because protein samples in particular need to be collected, concentrated, and frozen quickly. It would also allow me to train the undergraduates that work in my lab how to collect samples. Having undergraduate assistance would ensure that samples would not be skipped or missed (which occurs if I am not present to collect the sample myself).

Ashley E. Maloney, Graduate Student, School of Oceanography

I am a graduate student in Chemical Engineering department, mainly working in the Benjamin Hall Interdisciplinary Research Building. Part of my project is doing metabolomics using LCMS, which involves sample preparation and instrument time for chromatography separation. Currently, the sample preparation is done in Benjamin Hall, while the actual LCMS run is done in the Ocean Science Building where the instrumentation is located. The current workflow could be greatly improved by having a more efficient sample prep procedure in the Ocean and Sciences Building. Having everything in one place, especially in the zone where no C14 restriction applies would make sample prep easier and more efficient. Meanwhile, it could also save time in sample transportation, which would avoid potential degradation problems.

Yanfen Fu, Graduate Student, Chemical Engineering

As a graduate student in Civil and Environmental Engineering, I offer my support for this proposal and for the new instrumentation in the MMRC. Access to this lab with the current MS instrumentation as well as the new sample preparation equipment will benefit my current and future research. This center will allow future students, both undergraduate and graduate, to do their projects using innovative technology and research that will advance our knowledge on microbial metabolism.

Wei Qin, Graduate Student, Civil and Environmental Engineering

Items

Group Funded Item Unit price Quantity Subtotal
None

Beadbeater with cooling adapter

$11,671.20 1 $11,671.20
Description

FastPrep-24 5G Instrument with CoolPrep Sample Holder
Quote from MP Biomedicals

Justification

Needed for initial extraction of proteins and metabolites from cells. Samples are kept cold during extraction.

Bench top centrifuge

$15,403.57 1 $15,403.57
Description

Allegra X-14R Refrigerated Benchtop Centrifuge
Quote from VWR

Justification

Major component in protein extraction protocol, removes insoluble material from metabolite and protein samples before running on mass spectrometers.

Reacti-Vap Evaporator

$724.13 1 $724.13
Description

Thermo Scientific 9 port evaporator (TS-18825)
Quote from VWR

Justification

Needed for removing solvents after extraction and concentrating samples before running on mass spectrometers.

Fluorometer

$1,664.00 1 $1,664.00
Description

Quantus fluorometer
Quote from Promega

Justification

Measures total protein concentration in samples after extraction.

Incubator with shaker tables

$6,632.63 1 $6,632.63
Description

Heratherm Advanced Protocol Microbiological Incubators, 180L
Quote from VWR, Supplier is Thermo Scientific

Justification

Needed for growing cultures of bacteria and archaea under controlled temperature and light that are needed for ensuring reproducibility of data and standard materials.

SPE Vacuum Manifold System with vacuum pump

$2,449.61 1 $2,449.61
Description

24 port vacuum manifold system for solid phase extraction columns
Quote from VWR, Supplier is Grace Division for manifold
Quote from Sterlitech for vacuum pump

Justification

Solid phase extraction columns and vacuum manifold are needed for concentrating metabolites from filtered seawater or culture media and getting rid of salt in order to measure dissolved metabolites on mass spectrometers.

pH Meter with microelectrode

$1,665.00 1 $1,665.00
Description

29130110 pH Meter with 125 mm microelectrode
Quote from Metrohm

Justification

Needed for measuring pH of samples during protein and metabolite extractions. Appropriate pH will allow for complete extraction of both proteins and metabolites. Also needed for preparing solvents for LCMS.

Analytical Balance

$4,821.93 1 $4,821.93
Description

XS Series Analytical Balance, METTLER TOLEDO
Quote from VWR

Justification

Needed for weighing out small amounts of protein and metabolite standards and samples.

Peristaltic Pump

$1,980.00 1 $1,980.00
Description

Masterflex L/S Digital Drive, 600 RPM, 115/230 VAC
Quote from Cole-Parmer

Justification

Needed for filtering culture and environmental samples.

Pressure Cell for analytical column packing

$1,412.00 1 $1,412.00
Description

Pressure cell for analytical column packing
Quote from UW Proteomics Resource (UWPR)

Justification

Allows for the in-house packing of analytical columns for analyzing proteins on mass spectrometers. This is more cost-effective than purchasing commercially available columns which cost ~$1000 each.

Laser-Based Micropipette Puller

$17,155.00 1 $17,155.00
Description

P-2000 Laser-Based Micropipette Puller
Quote from Sutter Instrument

Justification

Allows for the in-house packing of analytical columns for analyzing proteins on mass spectrometers. This is more cost-effective than purchasing commercially available columns which cost ~$1000 each.

Freight and Tax

$6,557.91 1 $6,557.91
Description

Freight and Tax

Justification

Freight and Tax

Total requested: $72,136.98

Total funded: $72,136.98

Group Funded Item Change in Unit price Change in Quantity Change in Subtotal
None

Peristaltic Pump with pump heads

$3,176.04 1 $3,176.04
Description

Masterflex L/S Digital Drive, 600 RPM, 115/230 VAC
Masterflex L/S Rigid PTFE-Tubing Pump Head
Quote from Cole-Parmer

Justification

Needed for filtering culture and environmental samples. We have already purchased one of these pumps with money from the STFC. This pump has already been used in our lab and out in the field on a research cruise. Sample processing for metabolomics and proteomics needs to happen quickly since due to the sensitive nature of the samples and having a second pump will allow us to process twice as many samples in the same amount of time.

Teflon bottles

$1,018.24 1 $1,018.24
Description

Nalgene 2 liter Teflon sample collection bottles (4 bottles for this price).
Quote from VWR

Justification

Regular plastic bottles have the potential to leach plastics into the water we collect, therefore contaminating our samples. The plastic contamination can interfere with the measurement of proteins and metabolites. Teflon bottles are meant for high-purity analysis and will not contaminate the water that we collect for proteomics and metabolomics.

Microcentrifuge

$6,931.76 1 $6,931.76
Description

Microcentrifuge 5424R, with Rotary Knobs, Refrigerated -10° to 40°C
Quote from VWR

Justification

Needed for removing insoluble material from metabolite and protein samples before running on mass spectrometers. During method development, we have discovered the need to spin smaller tubes at a faster rate than is allowed by the regular bench top centrifuge. Having this microcentrifuge in addition to the regular centrifuge will allow us greater flexibility in sample size and the rate at which samples need to be spun down.

Supplemental request: $11,126.04

Decision: Not funded

Group Funded Item Unit price Quantity Subtotal
None

Beadbeater with cooling adapter

$11,671.20 1 $11,671.20
Description

FastPrep-24 5G Instrument with CoolPrep Sample Holder
Quote from MP Biomedicals

Justification

Needed for initial extraction of proteins and metabolites from cells. Samples are kept cold during extraction.

Bench top centrifuge

$15,403.57 1 $15,403.57
Description

Allegra X-14R Refrigerated Benchtop Centrifuge
Quote from VWR

Justification

Major component in protein extraction protocol, removes insoluble material from metabolite and protein samples before running on mass spectrometers.

Reacti-Vap Evaporator

$724.13 1 $724.13
Description

Thermo Scientific 9 port evaporator (TS-18825)
Quote from VWR

Justification

Needed for removing solvents after extraction and concentrating samples before running on mass spectrometers.

Fluorometer

$1,664.00 1 $1,664.00
Description

Quantus fluorometer
Quote from Promega

Justification

Measures total protein concentration in samples after extraction.

Incubator with shaker tables

$6,632.63 1 $6,632.63
Description

Heratherm Advanced Protocol Microbiological Incubators, 180L
Quote from VWR, Supplier is Thermo Scientific

Justification

Needed for growing cultures of bacteria and archaea under controlled temperature and light that are needed for ensuring reproducibility of data and standard materials.

SPE Vacuum Manifold System with vacuum pump

$2,449.61 1 $2,449.61
Description

24 port vacuum manifold system for solid phase extraction columns
Quote from VWR, Supplier is Grace Division for manifold
Quote from Sterlitech for vacuum pump

Justification

Solid phase extraction columns and vacuum manifold are needed for concentrating metabolites from filtered seawater or culture media and getting rid of salt in order to measure dissolved metabolites on mass spectrometers.

pH Meter with microelectrode

$1,665.00 1 $1,665.00
Description

29130110 pH Meter with 125 mm microelectrode
Quote from Metrohm

Justification

Needed for measuring pH of samples during protein and metabolite extractions. Appropriate pH will allow for complete extraction of both proteins and metabolites. Also needed for preparing solvents for LCMS.

Analytical Balance

$4,821.93 1 $4,821.93
Description

XS Series Analytical Balance, METTLER TOLEDO
Quote from VWR

Justification

Needed for weighing out small amounts of protein and metabolite standards and samples.

Peristaltic Pump

$1,980.00 1 $1,980.00
Description

Masterflex L/S Digital Drive, 600 RPM, 115/230 VAC
Quote from Cole-Parmer

Justification

Needed for filtering culture and environmental samples.

Pressure Cell for analytical column packing

$1,412.00 1 $1,412.00
Description

Pressure cell for analytical column packing
Quote from UW Proteomics Resource (UWPR)

Justification

Allows for the in-house packing of analytical columns for analyzing proteins on mass spectrometers. This is more cost-effective than purchasing commercially available columns which cost ~$1000 each.

Laser-Based Micropipette Puller

$17,155.00 1 $17,155.00
Description

P-2000 Laser-Based Micropipette Puller
Quote from Sutter Instrument

Justification

Allows for the in-house packing of analytical columns for analyzing proteins on mass spectrometers. This is more cost-effective than purchasing commercially available columns which cost ~$1000 each.

Freight and Tax

$6,557.91 1 $6,557.91
Description

Freight and Tax

Justification

Freight and Tax

Overall total funded: $72,136.98

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