Archived News & Events
This page contains archived news and event info. For up-to-date information, see the Current News & Events page
July 14, 2012
The Mass Spectrometry Special Interest Group (MS-SIG) held a symposium in Long Beach, California featuring prominent researchers in the field of proteomics, including Richard D. Smith, Michael MacCoss, Olga Vitek, Alexey Nesvizhskii, and Bobbie-Jo Webb-Robertson. This one day symposium, occured just prior to the ISMB 2012 conference, which focused on:
- Label vs. label-free protein quantification
- Proteomics applications in biology and medicine.
May 3 - 5, 2008
The 8th annual International Conference of the Canadian Proteomics Inititiative (CPI 2008) will be held in Vancouver, British Columbia. This 4-day conference includes workshops, invited speakers (including Joshua Adkins), and poster sessions. Topics include human and clinical proteomics, membrane & receptor proteomics, plant and animal proteomics, structural proteomics, and bioinformatics.
March 16, 2008
Members of the Biological Separations & Mass Spectrometry group of the Environmental Molecular Science Laboratory (EMSL) presented a short course on "Data Extraction and Analysis for LC-MS Based Proteomics" at the 4th Annual US HUPO Conference. The session was a refinement and expansion of last year's course, discussing various aspects of label-free quantitative proteomics using LC-MS analysis platforms. The PDF of this course is available on the Workshop Page.
June 3 - 7, 2007
DeconMSn - A Software Tool for Determination of Accurate Monoisotopic Masses of Parent Ions of Tandem Mass Spectra developed with the NCRR support was presented in a poster session at the 55th ASMS Conference on Mass Spectrometry. This tool can more accurataly detect the monoisotopic masses to provide improved peptide identifications for high precursor mass resolution data. Initial results show promising improvements in peptide identification.
March 5, 2007
Members of the Biological Separations & Mass Spectrometry group of the Environmental Molecular Science Laboratory (EMSL) organized a short course on Data Extraction and Analysis for LC-MS Based Proteomics at the 3rd Annual US HUPO Conference. The session focused on the use of two different LC-MS data extraction and analysis platforms for higher-throughtput proteomics. Many tools that are listed here were used and disseminated. The PDF of this course is available on the Workshop Page.
May 28 - June 1, 2006
The 2006 annual American Society for Mass Spectrometry (ASMS) conference will be taking place at the Washington State Convention & Trade Center in Seattle, Washington. Members of the Biological Separations & Mass Spectrometry group of the Environmental Molecular Science Laboratory (EMSL) will be making a significant contribution to the conference in the form of twenty-one poster presentations and four talks. Discussions will range from tools required for implementation of the Accurate Mass Tag (AMT) pipeline used in protein identification to label-free comparative study of phosphatase inhibitor-induced phosphoproteomics using targeted analysis.
June 20 - June 21, 2005
The annual Northwest Symposium for Systems Biology took place on the Pacific Northwest National Laboratory campus in Richland, Washington. The title of this year's symposium was "Toward A Predictive Science". This symposium focused on the process of driving systems biology toward the ability to predict complex biological systemic behaviors via three engaging sessions: Generating the Data Needed for Prediction; Generating Models that Predict; and Applications: Brave New world.
March 31 - April 1, 2005
In conjunction with hosting a Proteome Society Meeting in the spring of 2005, the Proteomics Research Resource for Integrative Biology hosted a Separations and Mass Spectrometry Applied to Proteomics and the Informatics Challenges Workshop that focused on proteomic data standards and informatics challenges. We hope to have minutes from that meeting available soon, and you are welcome to peruse the agenda for these events for abstracts of the presentations.
- Clustering is Key to Lighting Up the Dark Proteome, Spectral archives let researchers leverage unidentified spectra (2011).
- Top-to-Bottom Protein Characterization, Pressurized pepsin digestion as an automatable alternative to trypsin (2011).
- Unique Spinal Fluid Proteins Found in Chronic Fatigue, Lyme Disease Syndrome Patients (2011).
- In collaboration with Patrick S. Moore and his research team at the University of Pittsburgh Cancer Institute, BTRR scientists contributed to characterizing viral gene expression using a systems biology approach. BTRR-generated proteomics data were coupled to transcriptomics measurements providing a comprehensive view of viral gene expression. The results, published in BMC GENOMICS, have achieved the "Highly accessed" designation relative to age at BioMed Central. (2011).
- "Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes"
Lindsay R Dresang, Jeremy R Teuton, Huichen Feng, Jon M Jacobs, David G Camp II, Samuel O Purvine, Marina A Gritsenko, Zhihua Li, Richard D Smith, Bill Sugden, Patrick S Moore, and Yuan Chang.
BMC Genomics, 12:625-639 (2011).
Abstract on BioMed Central
- "Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes" Lindsay R Dresang, Jeremy R Teuton, Huichen Feng, Jon M Jacobs, David G Camp II, Samuel O Purvine, Marina A Gritsenko, Zhihua Li, Richard D Smith, Bill Sugden, Patrick S Moore, and Yuan Chang. BMC Genomics, 12:625-639 (2011).
- Identifying the Degradome, Protein pieces provide path toward early detection of breast cancer (2010).
- Thousands of New Proteins Discovered in Spinal Fluid, Research establishes healthy benchmark to aid in understanding neurological disorders (2010).
- Novel Indicators of Oxidative Stress in Disease, Proteomic study offers clue to how diseases such as Parkinson’s progress (2010).
- New Analytical Platform is Making the Nearly Impossible Routine (2010).
- Making Needles in the Haystack Easier to Find, Online protein separation strategy helps detect low-abundance proteins (2009).
- Recent Patents Describes a New Method to Separate and Characterize Ions, Scientists’ approach employs time-dependent electric field with novel waveform profiles (2009).
- TImproved Protein Separations Systems Developed by PNNY and Biotech Firm, Tandem system uses antibodies from chicken eggs to find low-abundance proteins that indicate disease (2009).
- New SPIN Corrals Protein Molecules, PNNL technology boosts mass spectrometer sensitivity and performance (2008).
- Proteins Under Pressure, A little pressure in proteomics analyses squeezes four hours into a minute (2008).
- Assigning Proteins ID Cards, New approach identifies proteins with confidence, dropping false identifications to near zero (2008).
- Molecular-level Analyses Reveal Possible Mechanisms Underlying Parkinson’s Disease (2008).
- New Technology Enables Better Understanding of Brain Development (2008).
- Dick Smith Named to Prestigious 2007 Scientific American 50 List (2007).
- Researchers Develop, Improve and Enhance Technologies for Rapid Analysis of Complex Samples (2007).
- Two Journal Articles Make ACS Most-Cited List (2007).
- First in Mouse and Mammalian Brain Proteomic Research Featured in Journal (2006).
- PNNL Featured in C&E News Sys Bio Cover Story (2006).
- PNNL Team Makes the First Global Identification of Endogenous Levels of Nitrated Proteins in the Brain (2006).
- Better proteomic measurements achieved with smaller liquid chromatography columns (2006).
- Combined methods meet challenge of studying protein changes (2006).
- Simulation of PNNL Protein Identification Process Featured in Journal Special Edition (2005).
- Journal lists two PNNL articles in top five most accessed (2005).
- Cutting-edge proteomics tool featured in two Analytical Chemistry articles (2005).
- Ultra-high performance separations and mass spectrometry work featured in IJMS (2005).
- Collaborative research published in PNAS focuses on skeletal muscle cell understanding (2005).
Awards & Honors
- Wei-Jun Qian, BTRR scientist, was named winner of a Presidential Early Career Award for Scientists and Engineers (PECASE) for his work in proteomics. The PECASE is the highest honor given by the U.S. government to scientists and engineers who are at the start of their careers. Qian and his fellow PECASE winners were honored at a White House ceremony on October 14, 2011. View Article
- Dr. Keqi Tang receives Outstanding Mentor Award. View Article
- Three Pacific Northwest National Laboratory scientists took the first, fourth, and eighth slots on the 10 Most Prolific Authors list for the first 10 years of the JOURNAL OF PROTEOME RESEARCH. Investigators recognized by ACS include BTRR PI Richard D. Smith, number one on the list; BTRR Associate Director David G. Camp II, fourth on the list; and BTRR scientist Ronald J. Moore, eighth on the list. The Journal of Proteome Research is one of the top 10 journals in the field of biochemical research methods. View Article
- Spinal Fluid Research Wins Gordon Battelle Prize View Article
- BTRR scientists Alex Shvartsburg and Keqi Tang, and BTRR PI Richard D. Smith are developers, with Owlstone Nanotech, of the Ion Mobility Spectrometer on a Microchip, which won a 2010 R&D 100 Award. View Article
- Dr. Richard Smith elected to second term on HUPO Board View Article
- BTRR PI Richard D. Smith was named 2010 Scientist of the Year by R&D Magazine. He is the first scientist from a Department of Energy national laboratory to receive this honor. This award, now in its 45th year, recognizes leading researchers who are making significant contributions to science. Smith is being recognized for his pioneering work in effectively combining the development of new technology with its application to biological systems to gain new insights. He received the award at the 2010 R&D 100 Gala Awards Banquet November 11, 2010 in Florida. View Article
- BTRR PI Richard D. Smith was elected to the Washington State Academy of Sciences in 2010 for an outstanding record of scientific accomplishments and national and international recognition. His contributions in the fields of proteomics, mass spectrometry, and separations science have led to advances in health, energy, the environment and national security. The Academy was created in 2005 to provide scientific and engineering analysis to inform public policy-making for the state. View Article
- Dr. Richard Smith selected for Analytical Chemistry Award View Article
- BTRR PI Richard D. Smith was named one of 12 Best and the Brightest Innovators in the Energy Labs in the April/May 2010 issue of Innovation, a journal of technology commercialization. The article "Dick Smith: A Most Prolific Inventor" can be viewed Innovation.
- BTRR PI Richard D. Smith, and BTRR scientists Ryan Kelly, Jason Page, and Keqi Tang won a 2009 R&D 100 Award for the Ultrasensitive Electrospray Ionization Mass Spectrometry Source and Interface. The device integrates four patented or patent pending technologies to provide greater sensitivity and precise measurements while requiring smaller samples. The awards are given by R&D Magazine for the 100 most technologically significant products introduced the past year. View Article
- Dr. Richard Smith named Editor-in Chief of Journal of Proteomics & Bioinformatics View Article
- BTRR PI Richard D. Smith received the 2009 Human Proteome Organization Discovery Award in Proteomics Sciences. HUPO is an “international scientific organization representing and promoting proteomics through international cooperation and collaborations.” Smith is a member of HUPO’s International Executive Committee (the equivalent of a Board of Directors). In accepting this award, Smith attended the HUPO 8th Annual World Congress in Toronto, September 26-30, 2009, and presented a major lecture. View Article
- Richard D. Smith, BTRR PI, Battelle Fellow, and Chief Scientist, was named Pacific Northwest National Laboratory Inventor of the Year for Fiscal Year 2008 in May of 2009. The PNNL Inventor of the year award recognizes innovation that has resulted in the creation of intellectual property or the potential to create intellectual property. Smith has taken part in developing and applying advanced analytical methods and instrumentation, with an emphasis on high-resolution separations and mass spectrometry, to biomedical, biological, and environmental research. He is recognized as a world leader in this area. View Article
- Wei-Jun Qian, BTRR scientist, was one of 30 "rising young stars" named by Genome Technology magazine in its third annual "Tomorrow's PIs" special edition. The magazine offers readers a chance to see large-scale biological research through the eyes of some of the best and the brightest young scientists who are poised to make significant contributions to their areas of interest. Qian, a senior scientist at Pacific Northwest National Laboratory, is an expert in the rapidly growing field of proteomics. An interview with Qian entitled "Step by Step, a Better Mass Spec" appears in the December 2008/January 2009 issue of Genome Technology. View Article
- Proteomics research makes Journal Top 20 List of Most Cited View Article
- Keqi Tang, BTRR scientist, was named Pacific Northwest National Laboratory Inventor of the Year for Fiscal Year 2007 in April of 2008. The PNNL Inventor of the year award recognizes innovation that has resulted in the creation of intellectual property or the potential to create intellectual property. Tang is known as a hands-on inventor who diligently ensures that conceptual ideas are implemented in working instruments. He has focused on the design, fabrication and testing of new ion sources, ion optics systems, and gas phase separation methods to improve sensitivity and resolution in mass spectrometry. Tang's intellectual property has garnered 8 licenses with commercial firms. View Article
- Mass spectrometry manuscript heads top 25 hottest articles list View Article
- Dr. Richard Smith elected to HUPO Council View Article
- Dr. Wei-Jun Qian honored with Ronald L. Brodzinski Award for Early Career Exceptional Achievement View Article
- Proteomic Poster Wins Award at International Proteome Meeting View Article
- Dr. Richard Smith named AAAS Fellow View Article
For its potential to trim years off the time required to analyze a proteome, the FT-MS Proteome Express made the 2003 list of the world's 100 most important scientific and technical innovations, according to an annual competition by R&D Magazine.
FT-MS Proteome Express is an automated, ultra-high resolution combined separation and mass spectrometer-based system used to identify and detect the relative abundance of large and complex proteins. (FT-MS stands for Fourier-transform ion cyclotron resonance mass spectrometer.) PNNL researcher and Battelle Fellow Richard D. Smith was the principal investigator in its creation. Measuring proteins and their abundances at different times, and especially the proteins present in only tiny amounts, is the key to understanding molecular-level cell function and disease progression, treatment, and prevention. In experiments at PNNL, the Proteome Express has demonstrated more than 100-fold improvements in speed and sensitivity over previous methods, and demonstrated its applicability in projects that range from how microorganisms absorb atmospheric carbon to how certain viral proteins cause blindness.
Pictured at right are award recipients Dick Smith, Gordon Anderson, and Harold Udseth (l to r). This is Smith's seventh R&D 100 Award, and brings the PNNL R&D 100 Awards total to 62.Back to Top
The Peak Finder program is a LabView application (compiled to a Windows .Exe) that can be used to compute the peak capacity of chromatographic separations. The peak capacity is defined as the number of compounds that can be separated with baseline resolution in a given separation space. The Peak Finder uses a robust method for computing peak capacity, fitting all of the peaks in a chromatogram with a Gaussian peak, then computing the median peak width of each peak and dividing the separation space (time) by the median peak width. The user can step through the program and examine the fit for each peak, modifying the peak width and elution time for each peak so that the Gaussian peak best represents the actual peak. Peaks that the program found but are not real peaks can be excluded from the peak list and thus all subsequent calculations.
Decon2LS is a software tool useful for finding isotopic signatures of chemical entities in mass spectrometry data using algorithms such as THRASH, Mercury, etc. It works on profile mode data from several different instrument types and vendor formats and consists of the following modules in the engine for performing the deisotoping:
|1)||Readers: This module allows us to read different data formats with a uniform interface. There are classes for readers of data from Bruker, Agilent, Finnigan, mzXML and Micromass. These readers use vendor libraries to access the proprietary data formats from these vendors.|
|2)||PeakProcessor: Module for performing peak processing operations such as peak top discovery, smoothing of data, calculating peak statistics such as peak width at half max, signal to noise etc.|
|3)||ChargeDetection: Algorithms to detect charges of species using Autocorrelation.|
|4)||Deconvolution: Deisotoping is performed using a variant of the THRASH algorithm.|
In the beta version, we are releasing processing dlls and a binary version of the application to allow users to deisotope their data. The source code will be released soon.
Other than the processing engine, Decon2LS provides a user interface for the data and also makes available several high performance controls which can be reused by other applications to plot line and scatter charts.
The VIPER (Visual Inspection of Peak/Elution Relationships) software tool has been newly released to allow researchers to visualize and characterize the features detected during LC-MS analyses. It is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT Tag approach (see Zimmer, Monroe, Qian, & Smith, Mass Spec. Reviews, 2006, 25, 450-482).
The software allows one to display the data as a two-dimensional plot of spectrum number (i.e. elution time) vs. mass. It can read MS data from several file formats: .PEK, .CSV, .mzXML, and .mzData. VIPER can process a data file in an automated fashion to:
|1)||Load and filter the data|
|2)||Find features and their chromatographic peak profile by examining the data in two dimensions (mass and elution time), then using a data clustering algorithm to look for groups of related data|
|3)||Align the observed elution times of the features with the elution times of the expected peptides (i.e. MT tags)|
|4)||Refine the mass calibration using a histogram of the observed mass error values|
|5)||Match the features to the MT tags by comparing the mass and time values of the features to the mass and time values of the MT tags|
|6)||Export the results to a report file|
VIPER has a rich, full featured graphical user interface with numerous options for exploring the data and customizing the analysis parameters. It runs on Windows computers and requires Microsoft Access be installed to create and edit the MT tag databases. In order to view mass spectra from raw data files (e.g. Finnigan .Raw files, one will also need to install ICR-2LS. VIPER is a mature software application that has been in routine use at PNNL since 2003 and has been used to process over 15,000 datasets.
This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.
The MASIC (MS/MS Automated Selected Ion Chromatograms) software tool has been released as open source software (under the Apache, Version 2.0 license agreement). MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis. The SICs are generated using the LC-MS data (i.e. the MS1 spectra), then each SIC is processed using a peak finding algorithm to characterize the chromatographic peaks, providing peak statistics including elution time of the peak apex, peak area, peak signal/noise, and peak skew computed using statistical moments. The program can read Finnigan .Raw files, mzXML files, mzData files, or .cdf/.mgf combo files. Results are outputted both as flat files (.txt) and in an XML file that can be read using the accompanying graphical results browser. The browser provides a fast, graphical method for browsing the SICs identified by MASIC, allowing the user to sort and filter the SIC list as desired. MASIC has been in routine use in the PRISM pipeline since 2004 and has been used to process over 40,000 datasets.