Data by Organism
- Borrelia burgdorferi Data
- Deinococcus radiodurans Data
- Homo sapiens (human) Data
- Macaca nemestrina Data
- Mus Musculus (mouse) Data
Other Resources of Data Generated at PNNL
- Administrative Resource for Biodefense Proteomic Research Centers
- Biological and Environmental Research (BER) Data page with instructions on accessing the EDMS website at PNNL (part of the Biodemo project).
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.
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.
| 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. |
1.7 MB
(Excel file) |
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 to 130 MB) |
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. In press at the Journal of Chromatography B in May 2008. The Excel file contains the lipid metabolites identified by accurate mass, isotopic distribution, and MS/MS data, from both Positive and Negative ESI analysis. |
55 KB (Excel file) |
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. Submitted to the Journal of Proteome Research in January 2008. The .Zip file includes the supporting fragmentation spectra, identified peptides, and the SpectrumLook application for viewing the data. |
147 MB (.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. | 233 KB (.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. |
66 MB (.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. | 5.2 MB
(Excel file) |
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. |
507 MB (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. | 845 KB
(Excel file) |
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. |
159 MB (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). |
11 MB (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). | 11 MB (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). | 11 MB (ZIP) | 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 (electronic); (2006). | 667 KB
(Excel file) |
Download Data |
| 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. Submitted to the Journal of Proteome Research in December 2007. 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. |
6 MB (in six Excel files) |
Table 1 - 759 KB Table 2 - 4 MB Table 3 - 42 KB Table 4 - 1 MB Table 5 - 40 KB |
* Registration is required for all downloads, unless otherwise indicated.
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