Data

In addition to making data analysis software and tools available, the Resource provides raw and analyzed data. Extensive sets of capillary LC-MS/MS data are being made available to researchers interested in the analysis of such data, or needing access to such data sets to develop informatics tools. The spectra provide the basis for identification of large numbers of proteins from the organism, and are available to be "mined" for yet untapped information, e.g., on protein modifications.

Resources of Data Generated at PNNL

PNNL's Biological MS Data and Software Distribution Center (Omics.pnl.gov) contains a large selection of PNNL-generated raw data and processed results that you can browse and download. This site also hosts several PNNL-developed software tools, including source code.
The Resource Center for Biodefense Proteomic Research hosts Monkeypox, Salmonella typhimurium, Vaccinia, and Salmonella typhi data acquired at PNNL
PNNL's Biological and Environmental Research (BER) Data page contains instructions for accessing the Shewanella oneidensis data hosted on PNNL's Experimental Data Management System (EDMS) website at PNNL

Acknowledgment

All publications that result from the use of this data should include the following acknowledgment statement:

"Results are from experimental data that were obtained by Richard D. Smith and the Biological Systems Analysis and Mass Spectrometry group at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. Portions of this research were supported by the NIH National Center for Research Resources (RR18522), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830."

Disclaimer

Please note that while we have attempted to ensure the accuracy of all data presented here, the NCRR and PNNL own no liability for the use of results, data or information that have been provided through this server. Neither the use for commercial purposes, nor the redistribution of this raw data files to third parties, nor the distribution of parts of files or derivative products to any third parties, is permitted.

Borrelia burgdorferi

Supplemental data to 2005 publication	Used in Publication: "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia Burgdorferi." Jon M. Jacobs, X Yang, BJ Luft, JJ Dunn, DG Camp, and RD Smith. Proteomics; (2005) 5, 1446-1453.	1.7MB (Excel)	Download Data

Supplemental data to 2005 publication

Used in Publication: "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia Burgdorferi." Jon M. Jacobs, X Yang, BJ Luft, JJ Dunn, DG Camp, and RD Smith. Proteomics; (2005) 5, 1446-1453.

1.7MB
(Excel)

Download Data

Deinococcus radiodurans

Mass Spectral Data	The data was produced during the proteomic investigation of Deinococcus radiodurans MR-1, gram-positive bacteria with remarkable radiation tolerance. The mass spectral data provided here were generated by proteolytically digesting samples of D. radiodurans proteins grown under controlled conditions, then separating the digested samples by high-pressure microcapillary liquid chromatography (LC). The LC systems were coupled with ThermoFinnigan LCQ (Classic, Duo, or DecaXP) ion trap mass spectrometers. The files contained here are the unprocessed data from these instruments, in Thermo Xcalibur format, and can be viewed using our downloadable ICR-2LS software.	63 ZIP files (ranging from 37MB - 130MB)	Download Data

Mass Spectral Data

The data was produced during the proteomic investigation of Deinococcus radiodurans MR-1, gram-positive bacteria with remarkable radiation tolerance. The mass spectral data provided here were generated by proteolytically digesting samples of D. radiodurans proteins grown under controlled conditions, then separating the digested samples by high-pressure microcapillary liquid chromatography (LC). The LC systems were coupled with ThermoFinnigan LCQ (Classic, Duo, or DecaXP) ion trap mass spectrometers. The files contained here are the unprocessed data from these instruments, in Thermo Xcalibur format, and can be viewed using our downloadable ICR-2LS software.

63 ZIP files
(ranging from 37MB - 130MB)

Download Data

Homo sapiens (human)

Supplemental data for EGF time course publication (Registration not required)	Used in Publication: "Systems Analysis of Human Mammary Epithelial Cell Response through Integration of Gene Expression and Proteomic Data." Katrina M. Waters, T Liu, RD Quesenberry, WJ Qian, AR Willse, S Bandyopadhyay, LE Kathmann, TJ Weber, RD Smith, HS Wiley, and BD Thrall. Submitted to Genome Research in May 2009 The Excel file contains information of the datasets used in the study, 16O/18O peptide pairs quantified in each dataset from the cysteinyl and non-cysteinyl peptide fractions, and proteins from which those peptides originated.	2.9MB (Excel)	Download Data
Supplemental data to Serine/Threonine PP5 publication (Registration not required)	Used in Publication: "Novel Ser/Thr Protein Phosphatase 5(PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis" Bryan M. Ham, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp II, S Rossie, and RD Smith. Submitted to Journal of Proteome Research in Fall 2009 The .Zip file includes the supporting fragmentation spectra, identified peptides, and the SpectrumLook application for viewing the data.	147MB (.Zip file)	Download Data
Supplemental data to Human Lipid Profiling publication (Registration not required)	Used in Publication: "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Jie Ding, CM Sorensen, N Jaitly, H Jiang, DJ Orton, ME Monroe, RJ Moore, RD Smith, and TO Metz. Journal of Chromatography B; (2008) 871 (2), 243-252. The Excel file contains the lipid metabolites identified by accurate mass, isotopic distribution, and MS/MS data, from both Positive and Negative ESI analysis.	55KB (Excel)	Download Data
Supplemental data to HeLa Cell Phosphoproteome publication (Registration not required)	Used in Publication: "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Bryan M. Ham, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, D Orton, J Adkins, DG Camp II, S Rossie, and RD Smith. Journal of Proteome Research; (2008) 7 (6), 2215-2121. The .Zip file includes the supporting fragmentation spectra, identified peptides, and the SpectrumLook application for viewing the data.	146MB (.Zip file)	Download Data
Supplemental data to Mitotic Phsphorylation Motif publication (Registration not required)	Used in Publication: "Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus." Feng Yang, DG Camp II, MA Gritsenko, Q Luo, RT Kelly, TRW Clauss, WR Brinkley, RD Smith, and DL Stenoien. Journal of Cell Science; (2007) 120, 4060-4070.	233KB (.Zip file containing two Excel files)	Download Data
Supplemental data to Phosphoprotein Phosphatase (PPP) publication (Registration not required)	Used in Publication: "Applying a Targeted Label-Free Approach Using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Feng Yang, N Jaitly, H Jayachandran, Q Luo, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, HR Udseth, RD Smith, and S Rossie. Journal of Proteome Research; (2007) 6, 4489-4497. The .Zip file includes the supporting fragmentation spectra, identified peptides, and the SpectrumLook application for viewing the data.	66MB (.Zip file)	Download Data
Supplemental data to Human Pancreatic Islets publication	Used in Publication: "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Thomas O. Metz, JM Jacobs, MA Gritsenko, G Fontes, WJ Qian, D Camp II, V Poitout, RD Smith. Journal of Proteome Research; (2006) 5 (12), 3345-3354.	5.2MB (Excel)	Download Data
Proteome Probability Study Data	Used in Publication: "Probability-Based Evaluations of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Wei-Jun Qian, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp II, and RD Smith. Journal of Proteome Research; (2005) Jan-Feb; 4 (1), 53-62. The archive of 284 MS/MS analysis files are in the SEQUEST .dta format, but have been concatenated to a single text file per analysis. A small, self installing program named Concatenated Text File Splitter (Windows format) will unpack the concatenated analysis text files.	507MB (ZIP)	Download Data
Supplemental data to Liver Cell Proteomics publication	Used in Publication: "Proteome Analysis of Liver Cells Expressing a Full-length Hepatitis C Virus (HCV) Replicon and Biopsies of Post-transplanted Liver from HCV-infected Patients." Jon M. Jacobs, DL Diamond, EY Chan, MA Gritsenko, W Qian, M Stastna, T Baas, DG Camp II, RL Carithers, Jr., RD Smith, and MG Katze. Journal of Virology; (2005) 79, 7558-7569.	845KB (Excel)	Download Data
Serum Study (2002) Mass Spectral Data	The archive contains the spectrum files from 94 sample analyses as well as a "ReadMe" text file that provides more information regarding the generation of this data. These spectrum files are in the SEQUEST .dta format, but have been concatenated to a single text file per analysis. A small, self installing program named Concatenated Text File Splitter (Windows format) will unpack the concatenated analysis text files. Used in Publication: "Toward a Human Blood Serum Proteome I: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Joshua N. Adkins, SM Varnum, KJ Auberry, RJ Moore, NH Angell, RD Smith, DL Springer, and JG Pounds. Molecular & Cellular Proteomics; (2002) 1, 947-955.	159MB (ZIP)	Download Data
IPI protein database (2004) (Registration not required)	The FASTA file includes the human International Protein Index (IPI) protein database (41,216 protein entries).	11MB (ZIP)	Download Data
IPI reversed protein database (2004) (Registration not required)	The FASTA file includes the reversed human International Protein Index (IPI) protein database (41,216 protein entries) created by reversing the order of amino acid sequences for each protein (the carboxyl terminus becomes the amino terminus, and vice versa).	11MB (ZIP)	Download Data
IPI reversed protein database (2004) (Registration not required)	The FASTA file includes the reversed human International Protein Index (IPI) protein database (41,216 protein entries) created by reversing the order of amino acid sequences for each protein (the carboxyl terminus becomes the amino terminus, and vice versa).	11MB (ZIP)	Download Data

Macaca nemestrina

Supplemental data to Influenza Virus-Infected Macaques publication	Used in Publication: "An Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." T Baas, CR Baskin, DL Diamond, A García-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoeven, S Proll, JM Jacobs, ZR Caldwell, MA Gritsenko, RR Hukkanen, DG Camp II, RD Smith, MG Katze. Journal of Virology; (2006) 80 (21), 10813-10828.	667KB (Excel)	Download Data

Supplemental data to Influenza Virus-Infected Macaques publication

Used in Publication: "An Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." T Baas, CR Baskin, DL Diamond, A García-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoeven, S Proll, JM Jacobs, ZR Caldwell, MA Gritsenko, RR Hukkanen, DG Camp II, RD Smith, MG Katze. Journal of Virology; (2006) 80 (21), 10813-10828.

667KB
(Excel)

Download Data

Mus Musculus (mouse)

Supplemental data to Mouse Pancreatic Islet Reference Proteome publication (Registration not required)	Used in Publication: "Characterization of the Mouse Pancreatic Islet Proteome and Comparative Analysis with Other Mouse Tissues." Vladislav A. Petyuk, WJ Qian, C Hinault, MA Gritsenko, M Singhal, ME Monroe, DG Camp, RN Kulkarni, and RD Smith. Journal of Proteome Research; (2008) 7 (8), 3114-3126. An extensive reference database for mouse pancreatic islet proteome resulting from comprehensive LC-MS/MS characterization. The tables contain all protein and peptide identifications with estimated abundances within the proteome, identified post-translationally modified peptides, a comparison of protein expression among various mouse tissues, and a set of proteins revealed to be specific to pancreatic islets only.	6MB (in six Excel files)	Table 1 - 759KB Table 2 - 4MB Table 3 - 42KB Table 4 - 1MB Table 5 - 40KB

Supplemental data to Mouse Pancreatic Islet Reference Proteome publication
(Registration not required)

Used in Publication: "Characterization of the Mouse Pancreatic Islet Proteome and Comparative Analysis with Other Mouse Tissues." Vladislav A. Petyuk, WJ Qian, C Hinault, MA Gritsenko, M Singhal, ME Monroe, DG Camp, RN Kulkarni, and RD Smith. Journal of Proteome Research; (2008) 7 (8), 3114-3126.

An extensive reference database for mouse pancreatic islet proteome resulting from comprehensive LC-MS/MS characterization. The tables contain all protein and peptide identifications with estimated abundances within the proteome, identified post-translationally modified peptides, a comparison of protein expression among various mouse tissues, and a set of proteins revealed to be specific to pancreatic islets only.

6MB (in six Excel files)

Table 1 - 759KB
Table 2 - 4MB
Table 3 - 42KB
Table 4 - 1MB
Table 5 - 40KB

* Unless otherwise indicated, registration is required to download this data.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated.