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National Alzheimer's Coordinating Center


http://www.alz.washington.edu/


A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity).

Keywords

alzheimer's disease, brain, clinical, database, disease, human, neuropathological, neuropathology, specimen, tissue

Related Condition

Alzheimer's disease, Dementing disorder, Dementia

Website Status

Last checked up

Parent Organization

University of Washington; Washington; USA

Abbreviation(s)

NACC

Related Application(s)

Research

Species

Human

Related Disease(s)

Alzheimer's disease, Dementing disorder, Dementia

Supercategory

Resource

Resource Type

SCR_007327, Biomaterial Supply Resource, Topical Portal, Database

Funding Information

NIH Blueprint for Neuroscience Research, National Institute on Aging U01 AG016976

Availability

Data are freely available to all researchers

Synonym(s)

National Alzheimer's Coordinating Center

Proper citation

National Alzheimer's Coordinating Center, RRID:SCR_007327

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PeptideAtlas: MassSpec

PeptideAtlas provides a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments collected for human, mouse, yeast, and several other organisms.

  • Records: 76
License Information:
PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. Results may be queried and browsed at the PeptideAtlas web site. The raw data, search results, and full builds can also be downloaded for other uses. ------------------------------------------------------------------------------------------------------------------------------------------------------------ FAQ: "How should I cite PeptideAtlas?" We thank you for citing PeptideAtlas in any publication that makes use of PeptideAtlas. You can find appropriate citations on our Publications page. FAQ: "What is public about your data?" The following sample record fields are made available if you you have specified minimum public access (private). 1: Institution, Contact, Date 7: Organism NCBI_TaxID (9606 for human) 11: Cell-type The spectra are not made available for the minimum public access (private) datasets. The following sample record fields are made available if you you have specified full public access. 1: Institution, Contact, Date 2: URL link to www resource 3: Literature PubMed ID 4: Experiment description 5: Treatment Description 6: Instrument type (LCQ, etc.) 7: Organism NCBI_TaxID (9606 for human) 8: Bio source description (eVOC) anatomical site 9: Developmental stage (eVOC) 10: Pathology (eVOC) 11: Cell-type 12: Date that we may make the raw data available to the public The spectra and data products are made available for the public access datasets. They are available at http://www.peptideatlas.org/repository If you have other questions, please send email, http://www.peptideatlas.org/feedback.php ------------------------------------------------------------------------------------------------------------------------------------------------------------ RAW DATA AVAILABLE FOR DOWNLOAD It is our policy to make publicly available for download as much of the raw data we use to build the PeptideAtlas as possible. This includes datasets that have been previously published or otherwise released by the data producers. If you download and use these data in a published work, please cite the associated article (or data contributors if unpublished); an acknowledgement of the PeptideAtlas repository would also be appreciated. There are also many unpublished raw datasets used to build the PeptideAtlas, and these are not made available for download until publication or release by the producers. ------------------------------------------------------------------------------------------------------------------------------------------------------------ PeptideAtlas Publications If you make use of any data or results from the PeptideAtlas project in a publication, please cite one or more of our PeptideAtlas papers: General publications General purpose citation: Desiere, et al., "The PeptideAtlas Project", Nucleic Acids Research, 2006, 34, D655-D658 Latest publication: Farrah, et al., The State of the Human Proteome in 2012 as Viewed through PeptideAtlas", Journal of Proteome Research, 2013, 12 (1), pp162-171 Intitial publication: Desiere, et al., "Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome", Genome Biology 2004, 6:R9 Tutorial: Farrah, et al., Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins , Serum/Plasma Proteomics, Methods in Molecular Biology, 2011 Publications regarding SRM SRMAtlas (whole proteome synthetic peptide SRM library) Initial publication (yeast): Picotti, et al., High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , Nat. Methods 7, 43-46 (2010) Yeast whole proteome: Picotti, et al., A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis, Nature 494 (7436):266-70 (2013) Human whole proteome: Kusebauch, et al. and Deutsch, et al. publications in preparation as of May 2013. SRM design (pre-SRMAtlas): Deutsch, et al., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , EMBO reports 9, 5, 429–434 (2008) PASSEL: Farrah, et al., PASSEL: the PeptideAtlas experiment library , Proteomics. 2012 Feb 9 Publications for specific species and sub-proteomes Human Plasma (latest): Farrah, et al., A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas , Mol Cell Proteomics (2011) Human Plasma (original): Deutsch, et al., "Human Plasma PeptideAtlas", Proteomics. 2005 Aug;5(13):3497-500 Mouse Plasma: Zhang, et al., A Mouse Plasma Peptide Atlas as a Resource for Disease Proteomics , Genome Biology, 9, 6, R93 (2008) . Cow: Bislev, et al., A Bovine PeptideAtlas of milk and mammary gland proteomes, Proteomics 2012, 12:18 . Honeybee: Queenie, et al., A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues, BMC Genomics 2011, 12:290. Halobacterium: Van, et al., Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage, J. Proteome Res.; 2008; ASAP Article; DOI: 10.1021/pr800031f. Yeast (S. cerevisiae): King, et al., "Analysis of the S. cerevisiae proteome with PeptideAtlas.", Genome Biol. 2006 Nov 13;7(11) DATA PUBLICATIONS The publications further describing datasets used in the PeptideAtlas builds can be found on the Raw Data Repository page and on the Data Contributors page.