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Events

July 14, 2012
The Mass Spectrometry Special Interest Group (MS-SIG) is holding 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, which occurs just prior to the ISMB 2012 conference, will focus on:

  1. Label vs. label-free protein quantification
  2. Proteomics applications in biology and medicine.

For more information, please see the ISMB Special Interest Group Meetings page and the MS-SIG 2012 website.

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.

Scientific Highlights

Software News

August 2006
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.

June 2006
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.

April 2006
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.

October 2005
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.

Awards & Honors

Award Recipients

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.

National Center for Research Resources (NCRR) National Institutes of Health (NIH)

Proteomics