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Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗

Test Rack Development for Extended Operation of Advanced Stirling Convertors at NASA Glenn Research Center

The U.S. Department of Energy (DOE), Lockheed Martin Space Company (LMSC), Sun power Inc., and NASA Glenn Research Center (GRC) have been developing an Advanced Stirling Radioisotope Generator (ASRG) for use as a power system on space science missions. This generator will make use of free-piston Stirling convertors to achieve higher conversion efficiency than currently available alternatives. NASA GRC's support of ASRG development includes extended operation testing of Advanced Stirling Convertors (ASCs) developed by Sunpower Inc. In the past year, NASA GRC has been building a test facility to support extended operation of a pair of engineering level ASCs. Operation of the convertors in the test facility provides convertor performance data over an extended period of time. Mechanical support hardware, data acquisition software, and an instrumentation rack were developed to prepare the pair of convertors for continuous extended operation. Short-term tests were performed to gather baseline performance data before extended operation was initiated. These tests included workmanship vibration, insulation thermal loss characterization, low-temperature checkout, and fUll-power operation. Hardware and software features are implemented to ensure reliability of support systems. This paper discusses the mechanical support hardware, instrumentation rack, data acquisition software, short-term tests, and safety features designed to support continuous unattended operation of a pair of ASCs.

Dugala, Gina M.↗

Relativistic ultrafast electron diffraction at high repetition rates

The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are being developed that are aimed at increasing the beam brightness in order to observe structural signatures, but so far they have been limited to low average current beams. Here, we present the technical design and capabilities of the HiRES (High Repetition-rate Electron Scattering) instrument, which blends relativistic electrons and high repetition rates to achieve orders of magnitude improvement in average beam current compared to the existing state-of-the-art instruments. The setup utilizes a novel electron source to deliver femtosecond duration electron pulses at up to MHz repetition rates for UED experiments. Instrument response function of sub-500 fs is demonstrated with < 100 fs time resolution targeted in future. We provide example cases of diffraction measurements on solid-state and gas-phase samples, including both micro- and nanodiffraction (featuring 100 nm beam size) modes, which showcase the potential of the instrument for novel UED experiments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Virtual Instrumentation for a Fiber-Optics-Based Artificial Nerve

A LabView-based computer interface for fiber-optic artificial nerves has been devised as a Masters thesis project. This project involves the use of outputs from wavelength multiplexed optical fiber sensors (artificial nerves), which are capable of producing dense optical data outputs for physical measurements. The potential advantages of using optical fiber sensors for sensory function restoration is the fact that well defined WDM-modulated signals can be transmitted to and from the sensing region allowing networked units to replace low-level nerve functions for persons desirous of "intelligent artificial limbs." Various FO sensors can be designed with high sensitivity and the ability to be interfaced with a wide range of devices including miniature shielded electrical conversion units. Our Virtual Instrument (VI) interface software package was developed using LabView's "Laboratory Virtual Instrument Engineering Workbench" package. The virtual instrument has been configured to arrange and encode the data to develop an intelligent response in the form of encoded digitized signal outputs. The architectural layout of our nervous system is such that different touch stimuli from different artificial fiber-optic nerve points correspond to gratings of a distinct resonant wavelength and physical location along the optical fiber. Thus, when an automated, tunable diode laser sends scans, the wavelength spectrum of the artificial nerve, it triggers responses that are encoded with different touch stimuli by way wavelength shifts in the reflected Bragg resonances. The reflected light is detected and a resulting analog signal is fed into ADC1 board and DAQ card. Finally, the software has been written such that the experimenter is able to set the response range during data acquisition.

Lyons, Donald R.↗

Satellite-Terrestrial Network Interoperability

The developing national and global information infrastructures (NII/GII) are being built upon the asynchronous transfer mode (ATM) telecommunications protocol and associated protocol standards. These protocols are themselves under development through the telecommunications standards process defined by the International Telecommunications Union (ITU), which as a body is sanctioned by the United Nations. All telecommunications manufacturers use these standards to create products that can interoperate. The ITU has recognized the ATM Forum as the instrument for the development of ATM protocols. This forum is a consortium of industry, academia, and government entities formed to quickly develop standards for the ATM infrastructure. However, because the participants represent a predominately terrestrial network viewpoint, the use of satellites in the national and global information infrastructures could be severely compromised. Consequently, through an ongoing task order, the NASA Lewis Research Center asked Sterling Software, Inc., to communicate with the ATM Forum in support of the interoperability of satellite-terrestrial networks. This year, Dr. Raj Jain of the Ohio State University, under contract to Sterling, authored or coauthored 32 explanatory documents delivered to the ATM Forum in the areas of Guaranteed Frame Rate for Transmission Control Protocol/Internet Protocol (TCP/IP), Available Bit Rate, performance testing, Variable Bit Rate voice over ATM, TCP over Unspecified Bit Rate+, Virtual Source/Virtual Destination, and network management. These contributions have had a significant impact on the content of the standards that the ATM Forum is developing. Some of the more significant accomplishments have been: (1) The adoption by the ATM Forum of a new definition for Message-In, Message-Out latency; and (2) Improved text (clearer wording and newly defined terms) for measurement procedures, foreground and background traffic, and scalable configuration in the latency and throughput sections of the Performance Testing Baseline Text.

vonDeak, Thomas C.↗

Testing Devices Garner Data on Insulation Performance

To develop a test instrument that could garner measurements of the thermal performance of insulation under extreme conditions, researchers at Kennedy Space Center devised the Cryostat 1 and then Cryostat 2. McLean, Virginia-based QinetiQ North America licensed the technology and plans to market it to organizations developing materials for things like piping and storage tank insulation, refrigeration, appliances, and consumer goods.

Source record↗

The I4 Online Query Tool for Earth Observations Data

The NASA Earth Observation System Data and Information System (EOSDIS) delivers an average of 22 terabytes per day of data collected by orbital and airborne sensor systems to end users through an integrated online search environment (the Reverb/ECHO system). Earth observations data collected by sensors on the International Space Station (ISS) are not currently included in the EOSDIS system, and are only accessible through various individual online locations. This increases the effort required by end users to query multiple datasets, and limits the opportunity for data discovery and innovations in analysis. The Earth Science and Remote Sensing Unit of the Exploration Integration and Science Directorate at NASA Johnson Space Center has collaborated with the School of Earth and Space Exploration at Arizona State University (ASU) to develop the ISS Instrument Integration Implementation (I4) data query tool to provide end users a clean, simple online interface for querying both current and historical ISS Earth Observations data. The I4 interface is based on the Lunaserv and Lunaserv Global Explorer (LGE) open-source software packages developed at ASU for query of lunar datasets. In order to avoid mirroring existing databases - and the need to continually sync/update those mirrors - our design philosophy is for the I4 tool to be a pure query engine only. Once an end user identifies a specific scene or scenes of interest, I4 transparently takes the user to the appropriate online location to download the data. The tool consists of two public-facing web interfaces. The Map Tool provides a graphic geobrowser environment where the end user can navigate to an area of interest and select single or multiple datasets to query. The Map Tool displays active image footprints for the selected datasets (Figure 1). Selecting a footprint will open a pop-up window that includes a browse image and a link to available image metadata, along with a link to the online location to order or download the actual data. Search results are either delivered in the form of browse images linked to the appropriate online database, similar to the Map Tool, or they may be transferred within the I4 environment for display as footprints in the Map Tool. Datasets searchable through I4 (http://eol.jsc.nasa.gov/I4_tool) currently include: Crew Earth Observations (CEO) cataloged and uncataloged handheld astronaut photography; Sally Ride EarthKAM; Hyperspectral Imager for the Coastal Ocean (HICO); and the ISS SERVIR Environmental Research and Visualization System (ISERV). The ISS is a unique platform in that it will have multiple users over its lifetime, and that no single remote sensing system has a permanent internal or external berth. The open source I4 tool is designed to enable straightforward addition of new datasets as they become available such as ISS-RapidSCAT, Cloud Aerosol Transport System (CATS), and the High Definition Earth Viewing (HDEV) system. Data from other sensor systems, such as those operated by the ISS International Partners or under the auspices of the US National Laboratory program, can also be added to I4 provided sufficient access to enable searching of data or metadata is available. Commercial providers of remotely sensed data from the ISS may be particularly interested in I4 as an additional means of directing potential customers and clients to their products.

Stefanov, William L.↗

Improved Instrumentation for Solar Resource Measurements and Forecasting: Cooperative Research and Development Final Report, CRADA Number CRD-09-349

Under this Agreement, NREL will work with Participant to improve the instrumentation and measurement systems available for measuring and monitoring solar radiation elements needed by the electric utilities and solar power system integrators to adequately characterize the spatial and temporal variations of the renewable energy resources. This work includes, but is not limited to, research and development for making cost effective radiometers, solar trackers, and related instrumentation for solar resource measurements and forecasting. Cooperative R&D is proposed in three areas: Improved radiometric systems for cost effective irradiance measurements (direct normal, global, diffuse and plane-of-array); evaluation of innovative disruptive technology approaches for deriving the constituent solar energy components utilizing new fast-response thermopile measurement technologies, coupled with innovative shading geometry and tracker motion control; and low-cost solutions for sky imaging needed for resource forecasting. This work will be conducted at NREL and Participant facilities.

14 SOLAR ENERGY↗

Historical Evolution of NASA Standard Materials Testing with Hypergolic Propellants and Ammonia (NASA Standard 6001 Test 15)

The NASA Johnson Space Center White Sands Test Facility (WSTF) has performed testing of hazardous and reactive aerospace fluids, including hypergolic propellants, with materials since the 1960s with the Apollo program. Amongst other test activities, Test 15 is a NASA standard test for evaluating the reactivity of materials with selected aerospace fluids, in particular hydrazine, monomethylhydrazine, uns-dimethylhydrazine, Aerozine 50, dinitrogen tetroxide oxidizers, and ammonia. This manuscript provides an overview of the history of Test 15 over a timeline ranging from prior to its development and first implementation as a NASA standard test in 1974 to its current refinement. Precursor documents to NASA standard tests, as they are currently known, are reviewed. A related supplementary test, international standardization, and enhancements to Test 15 are also discussed. Because WSTF was instrumental in the development and implementation of Test 15, WSTF experience and practices are referred to in this manuscript.

Greene, Benjamin↗

Update on Development of the Potassium-Argon Laser Experiment (KArLE) Instrument for In Situ Geochronology

Absolute dating of planetary samples is an essential tool to establish the chronology of geological events, including crystallization history, magmatic evolution, and alteration. We are addressing this challenge by developing the Potassium (K) -- Argon Laser Experiment (KArLE), building on previous work to develop a K-Ar in situ instrument. KArLE ablates a rock sample, determines the K in the plasma state using laser-induced breakdown spectroscopy (LIBS), measures the liberated Ar using quadrupole mass spectrometry (QMS), and relates the two by the volume of the ablated pit using laser confocal microscopy (LCM). Our goal is for the KArLE instrument to be capable of determining the age of several kinds of planetary samples to address a wide range of geochronolgy problems in planetary science.

Cohen, Barbara A.↗

Sofia Science Working Group

The purpose of this grant was to enable the Principal Investigator (P.I.) to travel to and participate in the meetings and activities of the NASA SOFIA Science Working Group (SSWG), and to spend time working on some of the associated technical issues relating to the SOFIA (Stratospheric Observatory for Infrared Astronomy) project. The SOFIA Science Working Group was established to help develop the plans and specifications for the next-generation airborne observatory ("SOFIA"), which is now under development. The P.I. was asked to serve on the SSWG due to his experience in airborne astronomy: he has developed several astronomical instruments for the Kuiper Airborne Observatory NASA's previous airborne astronomy platform (which was decommissioned in 1995 in preparation for SOFIA). SOFIA, which will be a 747 SP aircraft carrying a 2.7 meter diameter telescope, is a joint project sponsored by NASA and DLR (the German space agency), and is now under development by a consortium including Universities Space Research Association (USRA), Raytheon, Sterling Software, and United Airlines. Further details on the SOFIA project can be found on the internet at http: //sofia. arc. nasa. gov. Rather than develop the SOFIA observatory in-house, NASA decided to privatize the project by issuing a Request for Proposals (RFP). The respondents to this RFP were consortia of private organizations which together had the required facilities and expertise to be able to carry out the project; the winner was the group led by USRA. One of the main roles of the SSWG was to help develop the technical specifications for the SOFIA observatory. In particular, the SSWG provided advice to NASA on the specifications that were written into the RFP, particularly those which had an important impact on the scientific productivity of the observatory. These specifications were discussed at the meetings of the SSWG, which were held primarily at NASA/Ames (in California) and at NASA Headquarters (in Washington DC). Apart from these meetings, members of the SSWG were expected to perform more detailed analyses of the impact of certain parameters and specifications on the performance of astronomical instruments. The SSWG ended its activities with the selection of the USRA team in January 1997.

Zmuidzinas, J.↗

SOFIA Science Working Group

The SOFIA Science Working Group was established to help develop the plans and specifications for the next-generation airborne observatory ("SOFIA"), which is now under development. The P.I. has developed several astronomical instruments for the Kuiper Airborne Observatory, NASA's previous airborne astronomy platform (which was decommisioned in 1995 in preparation for SOFIA). SOFIA, which will be a 747 SP aircraft carrying a 2.7 meter diameter telescope, is a joint project sponsored by NASA and DLR (the German space agency), and is now under development by a consortium including Universities Space Research Association (USRA), Raytheon, Sterling Software, and United Airlines. Rather than develop the SOFIA observatory in-house, NASA decided to privatize the project by issuing a Request for Proposals (RFP). The respondents to this RFP were consortia of private organizations which together had the required facilities and expertise to be able to carry out the project; the winner was the group led by USRA. One of the main roles of the SSWG was to help develop the technical specifications for the SOFIA observatory. In particular, the SSWG provided advice to NASA on the specifications that were written into the RFP, particularly those which had an important impact on the scientific productivity of the observatory. These specifications were discussed at the meetings of the SSWG, which were held primarily at NASA/Ames (in California) and at NASA Headquarters (in Washington DC). Apart from these meetings, members of the SSWG were expected to perform more detailed analyses of the impact of certain parameters and specifications on the performance of astronomical instruments. The SSWG ended its activities with the selection of the USRA team in January 1997.

Zmuldzinas, J.↗

The 2010 AOP Workshop Summary Report

The rationale behind the current workshop, which was hosted by Biospherical Instruments Inc. (BSI), was to update the community and get community input with respect to the following: topics not addressed during the first workshop, specifically the processing of above-water apparent optical property (AOP data) within the Processing of Radiometric Observations of Seawater using Information Technologies (PROSIT) architecture; PROSIT data processing issues that have developed or tasks that have been completed, since the first workshop; and NASA instrumentation developments, both above- and in-water, that are relevant to both workshops and next generation mission planning. The workshop emphasized presentations on new AOP instrumentation, desired and required features for processing above-water measurements of the AOPs of seawater, working group discussions, and a community update for the in-water data processing already present in PROSIT. The six working groups were organized as follows: a) data ingest and data products; b) required and desired features for optically shallow and optically deep waters; c) contamination rejection (clouds), corrections, and data filtering; d) sun photometry and polarimetry; e) instrumentation networks; and f) hyperspectral versus fixed-wavelength sensors. The instrumentation networks working group was intended to provide more detailed information about desired and required features of autonomous sampling systems. Plenary discussions produced a number of recommendations for evolving and documenting PROSIT.

Hooker, Stanford B.↗

PACE Technical Report Series, Volume 5: Mission Formulation Studies

This chapter summarizes the mission architecture for the Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission, ranging from its scientific rationale to the history of its realized conception to itspresent-day organization and management. This volume in the PACE Technical Report series focuses ontrade studies that informed the formulation of the mission in its pre-Phase A (2014-2016; pre-formulation:define a viable and affordable concept) and Phase A (2016-2017; concept and technology development).With that in mind, this chapter serves to introduce the mission by providing: a brief summary of thescience drivers for the mission; a history of the direction of the mission to NASA's Goddard Space Flight Center (GSFC); a synopsis of the mission's and instruments' management and development structures; and a brief description of the primary components and elements that form the foundation ofthe mission, encompassing the major mission segments (space, ground, and science data processing) and their roles in integration, testing, and operations.

Cetinic, Ivona↗

Apollo Telescope Mount experiments technology

The Skylab Apollo Telescope Mount (ATM) experiments, consisting of a white light coronagraph, four ultraviolet instruments, two X-ray telescopes and two hydrogen-alpha telescopes, observed the sun daily for nine solar rotations. The results have only begun to be evaluated, but is is already apparent that many theories of solar physics will undergo significant revisions as results are further developed. The ATM instruments were individually larger, more complex, and provided better spatial resolution than previous solar satellite instruments. An additional major advantage of the telescope complex was its ability to simultaneously collect multispectral data for specific experiments. A description of the Skylab, the ATM and the ATM experiments will be given. The daily process of flight planning and execution will be described. Examples of scientific data and some preliminary findings will be presented.

Keathley, W. C.↗

Operations of Suborbital Research Platforms to Obtain Remote Sensing Data

The Armstrong Flight Research Center (AFRC) operates six highly modified aircraft in support the NASA science mission.These include two ER-2 aircraft, a DC-8, a G-III, and two Global Hawks. The NASA science missions demands that these aircraft be deployed around the globe while carrying a variety of science instruments. The ER-2 reconnaissance aircraft provides routine access to altitudes over 70,000 ft (20km) for large payloads and with an endurance of over 10hours. Recently the ER-2s have conducted convective storm research missions in the mid-western United States and supported the development of new instruments. The DC-8 is a four-engine jetliner that operates for up to 12 hours ataltitudes that range from the surface to 42,000 ft (13 km). Although its flight envelope is equivalent to conventional.

unmanned aerial platforms↗