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SRMAtlas specifications

Information


Unique identifier OMICS_02455
Name SRMAtlas
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Robert L. Moritz

Publications for SRMAtlas

library_books

N-Glycoprotein SRMAtlas

2013
PMCID: 3617325
PMID: 23408683
DOI: 10.1074/mcp.O112.026617

SRMAtlas citations

 (14)
library_books

Proteomic analysis of human lacrimal and tear fluid in dry eye disease

2017
Sci Rep
PMCID: 5645331
PMID: 29042648
DOI: 10.1038/s41598-017-13817-y

[…] a particular protein, with a length between 6 and 30 amino acids. To quantify the proteins, at least two peptides are selected and three product ions were selected. Optimized collisional energy from SRMAtlas database was applied in our dynamic MRM (dMRM) analysis. To validate the existence of target transitions, selected transitions of target proteins were tested with several MRM scans and transi […]

library_books

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

2017
Cell Syst
PMCID: 5493283
PMID: 28601559
DOI: 10.1016/j.cels.2017.05.009

[…] roteomics community. For example, the dataset can be used to generate high-quality and comprehensive spectral libraries for future proteomics experiments. In a recent publication presenting the Human SRMatlas, spectral libraries of 166,174 proteotypic tryptic peptides from all human protein-coding genes were generated by peptide synthesis and MS/MS analyses using quadrupole time-of-flight and trip […]

library_books

Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis

2017
PMCID: 5451515
PMID: 28580222
DOI: 10.5702/massspectrometry.A0056

[…] ides were selected from more than 30 candidate PTPs (6–25 amino acid residues) produced by trypsin digestion (Supplementary Table S1).,)After establishing comprehensive SRM assay methods, such as the SRMAtlas of human and yeast proteins,–) these methods could be reused owing to their basic compatibility among triple quadrupole mass spectrometers.) However, SRM assay methods for the targeted proteo […]

library_books

Database of Optimized Proteomic Quantitative Methods for Human Drug Disposition‐Related Proteins for Applications in Physiologically Based Pharmacokinetic Modeling

2017
PMCID: 5397556
PMID: 28074615
DOI: 10.1002/psp4.12170

[…] ighty‐four proteins were chosen as the most significant with regard to drug disposition. There proteins include 131 phase I DMEs, 66 phase II DMEs, 79 transporters, and 8 nuclear receptors (Figure ). SRMAtlas (Institute for Systems Biology, Seattle, WA) was used to predict the 10–20 best peptides for each protein, and the 10 best fragments from each peptide. These predicted peptide sequences were […]

library_books

Determination of differentially regulated proteins upon proteasome inhibition in AML cell lines by the combination of large‐scale and targeted quantitative proteomics

2016
Proteomics
PMCID: 5396343
PMID: 27709814
DOI: 10.1002/pmic.201600089

[…] d on shotgun analysis performed previously, their proteotypicity (i.e., specific, to the protein of interest), their reported frequency in proteomic data repositories such as Peptide Atlas and Human SRMAtlas . In total, three transitions per peptide were monitored resulting in a total of 1063 transitions (292 precursors, and 771 fragments) for the 66 targeted proteins (see Supporting Information […]

library_books

Exploring the potential of public proteomics data

2015
Proteomics
PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] the generated data. Several such generic repositories are now available, for example PRIDE , GPMDB , PeptideAtlas , and MassIVE (http://massive.ucsd.edu/ProteoSAFe) for shotgun results; and PASSEL , SRMAtlas (http://www.srmatlas.org), and Panorama for targeted proteomics quantification data. More specific databases have also been established, related to: diseases, for example TBDB for tuberculos […]

Citations

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SRMAtlas institution(s)
Institute for Systems Biology, Seattle, WA, USA; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Biognosys AG, Schlieren, Switzerland; Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Center for Infectious Disease Research, Seattle, WA, USA; Faculty of Science, University of Zurich, Zurich, Switzerland
SRMAtlas funding source(s)
Supported by the American Recovery and Reinvestment Act (ARRA) funds through National Institutes of Health, from the National Human Genome Research Institute grant RC2HG005805, the National Institute of General Medical Sciences under grant R01GM087221, S10RR027584 and 2P50 GM076547/Center for Systems Biology, the Luxembourg Centre for Systems Biomedicine/University Luxembourg, the European Research Council grant ERC-2008-AdG 233226 and ERC-2014-AdG 670821, the Swiss National Science Foundation (grant #31003A-130530), and a DAAD fellowship.

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