Aurum Data Set

The Aurum data set is a collection of commercially purchased proteins that have been checked for purity, tryptically digested, and analyzed using an ABI 4700 (MALDI TOFTOF) mass spectrometer. This data set is intended to be a reference set of spectra that can be used for many different purposes such as training computer algorithms or studying the fragmentation pathways of high-energy CID. The data set contains tryptic digests of over 246 known proteins, and each protein has been checked for purity using 1D gel analysis. Proteins in the Aurum data set were over expressed in E. Coli and purified using a sequence tag by Genway (San Diego, CA). The FASTA file included with this data set includes the NCBI nr protein sequence, as specified by Genway, with the appropriate sequence tag included.

Aurum is free to use. It is technically licensed under the popular open-source Apache 2.0 License, which means you can legally use commercially and non-commercially as you please. The only thing we ask in return is that you cite the Aurum manuscript. We encourage you to use this data set in any way that it may be helpful, but please acknowledge the work we did to put it on-line.

More information about the Aurum.

• Credits/Suggested Citation
• Download Options
• Aurum Tranche Link (Free download of the whole project + documentation) ^{What is Tranche?}
• Summary pages for each protein, includes sequence coverage, gel image(s), and identified peptides.
• Summary pages for the crap protein list from TheGPM.org
• FASTA Files
• FASTA file with the protein sequences: IPI_human_3.14.fasta
• Decoy FASTA file with the protein sequences and reverse sequences appended: IPI_human_3.14.fasta.decoy
• FASTA file with the crap proteins
• Search Results
• Mascot and Mascot w/var mod acrylamide adducts
• X!Tandem and X!Tandem w/var mod acrylamide adducts
• Sequest (HIS tag) and Sequest (HIS tag) w/var mod acrylamide adducts
• Sequest (T7 tag) and Sequest (T7 tag) w/var mod acrylamide adducts
• Scaffold Analysis Files: All Searches Combined, Mascot/Tandem/Sequest Combined, Mascot/Tandem/Sequest Separate, Mascot/Tandem/Sequest w/var mod acrylamide adducts Combined, and Mascot/Tandem/Sequest w/var mod acrylamide adducts Separate
• X!Tandem crap protein list search
• MS and MS/MS Data
• Peak List Data (one big .mgf file)
• Peak List Data (Separated by Plates)
• MS (PKL Format)
• T10467, T10475, T10622, T10645, T10707, T10739, T10761
• MSMS (MGF Format)
• T10467, T10475, T10622, T10645, T10707, T10739, T10761
• RAW Data (Separated by Plates)
• MS (PKL Format)
• T10467, T10622, T10645, T10707, T10739, T10761
• MSMS (T2D Format)
• T10467, T10622, T10645, T10707, T10739, T10761
• Help! How do I read this data?
• The links don't seem to work on-line?

Summary pages for each protein

We have attempted to provide several views of the Aurum data. The complete raw data including peak lists, spectra, FASTA files, decoy analysis results, and search engine results are available for those that wish to redo analysis of Aurum. A more user-friendly summary also exists for casual use. These pages quickly show you summary information about each protein in the Aurum data set. This includes sequence coverage, identified peptides, and PAGE gel images from our purity checks. The pages are designed to look good in a web browser. Try clicking a link below to see an example page.

Summary pages for crap proteins

Include with the aurum dataset is a simple crap(pronounced "cee-RAP") analysis of the analyzed proteins. The crap list is maintained by TheGPM.org and includes many of the common contaminent proteins that are seen in mass spec experiments. The table below provides links to summary pages for the proteins in the crap FASTA file.

This list is primarily intended to aid those who are trying to identify absolutely all of the spectra included with Aurum.

Credits/Suggested Citation

If you use the Aurum data set in any fashion, please cite the reference provided below. Proper citations help us justify efforts to continue developing and publishing data sets like Aurum.

Jayson A. Falkner, Donna M. Veine, Maureen Kachman, Angela Walker, John R.Strahler, and Philip C. Andrews, "Validated MALDI-TOF/TOF mass spectra for protein standards", JASMS, 2006

Support in part for this project was provided by the National Resource for Proteomics and Pathways (NRPP) and the Michigan Proteome Consortium (MPC, www.proteomeconsortium.org). This project is hosted freely on ProteomeCommons.org and the ProteomeCommons.org Tranche network as part of the National Resource for Pathways and Proteomics (NRPP) Grant # P41-RR018627.

Help! How do I read this data?

The goal of this project is to succinctly and accurately represent the data set. When possible we try to include the raw spectral information, along with any meaningful curation results. If you are having troubles reading the raw spectral data, please use the ProteomeCommons.org IO Framework's conversion utility to translate that data in to a usable format.

If you are having troubles reading either the spotting information or the curation results, please see the credits section and contact the appropriate person. Note that we do not provide free tech support nor will we interpret the data for your needs; however, we'll be happy to help answer simple questions in order to try and help you work with the data.

The links don't seem to work on-line?

The on-line links to directories may not show up as expected in you web browser. However, all the links work as expected if you download this project and read this documentation from your local computer. Please do this if you are having trouble using the links on-line.