Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Shotgun Protein Sequencing With Meta Contig Assembly

ABSTRACT: Guthals A, Clauser KR, Bandeira N. Mol Cell Proteomics 2012, 11, 1084-1096. doi:10.1074/mcp.M111.015768. Tranche_hash:s+8iy5TbHHydsOPmTf9yqotRGvkxeJPF8BXJxMxxZOnCRXqbje8wbn+Orpxr51YR3L0S2sZBTYljUdHUF35LjfTqeukAAAAAAv6xWQ==

PROVIDER: MSV000078501 | MassIVE | Thu Nov 21 13:46:00 GMT 2013

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

Shotgun protein sequencing with meta-contig assembly.

Guthals Adrian A Clauser Karl R KR Bandeira Nuno N

Molecular & cellular proteomics : MCP 20120713 10

Full-length de novo sequencing from tandem mass (MS/MS) spectra of unknown proteins such as antibodies or proteins from organisms with unsequenced genomes remains a challenging open problem. Conventional algorithms designed to individually sequence each MS/MS spectrum are limited by incomplete peptide fragmentation or low signal to noise ratios and tend to result in short de novo sequences at low sequencing accuracy. Our shotgun protein sequencing (SPS) approach was developed to ameliorate these ...[more]

PMID: 22798278

Similar Datasets

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics

Project description:Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong, SE, Jaffe JD, Carr SA. Mol Cell Proteomics 2012, mcp.M111.014423. doi:10.1074/mcp.M111.014423. Tranche_hash:5cHw5Rj36vYNshNpy8k4nojtPyW27N/FHcImna3+zw4QV6KIlLOg3i6zesWBdWkEX608MEgdxWuVyKvvdOgB9BAanesAAAAAAACEzw==

2013-11-20 | MSV000078495 | MassIVE

The matrisome: in silico definition and in vivo characterization of tumor extracellular matrix

Project description:Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. Mol Cell Proteomics 2012, 11: M111.014647. doi:10.1074/mcp.M111.014647. PMCID:PMC3322572. Tranche_hash:onoKvMCC9umP0dW2GlZSGN/DVfz6tqoyRvsA16h351RjGJZiqjk0wWGYQB9+zPpRj+ASAgKsd779N0Td4250FCPJ6jUAAAAAAABFoQ==

2013-11-20 | MSV000078494 | MassIVE

Shotgun protein sequencing: Assembly of MS/MS spectra from mixtures of modified proteins.

Project description:Bandeira N, Clauser KR, Pevzner PA. Mol Cell Proteomics, 2007, 6, 1123-1134. Tranche_Hash:eZfbmOVhNCNf1UbqPqrbqVvSiYgtlW9AjTGENk6VsFUedYjwjfJQ0sL5D6wbNiN9iFAEY0zPJY8qGtJJadXf/18XNZEAAAAAAAAG6g==

2013-11-20 | MSV000078493 | MassIVE

HEK293 Quality Control example dataset - contamination test

Project description:A simple HEK293 lysate, with two files containing a putative mycoplasma contamination, and two negative control samples, taken from Geiger etc al. (Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.) [PXD002395].

2015-11-04 | PXD003134 | Pride

11 human cell lines - Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

Project description:Re-submission of raw data from Geiger T et. al., Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.

2015-07-21 | PXD002395 | Pride

Architecture of the RNA polymerase II-Mediator core transcription initiation complex

Project description:Comparative Dynamic Transcriptome Analysis (cDTA) enables global analysis of newly synthesized RNA as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111) and reveals defects in transcription with much higher sensitivity than conventional steady-state methods. cDTA was carried out as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111), using the S. cerevisiae heterozygous Med17/med17delta strain (Euroscarf) transfected with plasmids pRS315-SRB4 or pRS315-srb4-ts as described in Larivi̬re et al. Nature. 2012 (DOI:10.1038/nature11670), and Y40343-wildtype (Euroscarf) or Med18-FRB-KanMX6 (Euroscarf) strains. Heatshock of SRB4 and srb4-ts strains was applied for 18 or 60 minutes at 37C prior to RNA labeling as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111). To deplete the Med18 subunit from the nucleus, anchor-away experiments were performed by rapamycin treatment (1 ug/ml in 200 mL YPD) for 18 or 60 minutes at 30C prior to RNA labeling as described in Sun et al. Mol. Cell. 2013 (DOI:10.1016/j.molcel.2013.09.010). Data analysis was as described in Sun et al. Genome Res. 2012 (DOI:10.1101/gr.130161.111).

2015-02-04 | E-MTAB-2942 | biostudies-arrayexpress

Shotgun protein sequencing with meta-contig assembly.

Project description: Not available

| S-EPMC3494147 | biostudies-literature

Optimal assembly for high throughput shotgun sequencing.

Project description: Not available

| S-EPMC3706340 | biostudies-literature

Clawing through evolution: Toxin diversification/convergence in the lineage Chilopoda (Centipedes)

Project description:Undheim EAB, Jones A, Clauser KR, Holland JW, Pineda SS, King GF, Fry BG. Mol Biol Evol, 2014 31: p?-?.

2014-04-02 | MSV000078573 | MassIVE

Plk1 Self-Organization and Priming Phosphorylation of HsCYK-4 at the Spindle Midzone

Project description:Burkard ME, Maciejowski J, Rodriguez-Bravo V, Repka M, Lowery DM, Clauser KR, Zhang C, Shokat KM, Carr SA, Yaffe MB, Jallepalli PV. PLoS Biology. 2009, 7, 1-16. PMCID: PMC2680336. Tranche_hash:hoZCdxyWctOiblTI0WPcWoNstEY2hXa1nrvH2/zm/8nMEni3uXsGtepf4XeqiDJTGfsP5zOmDl9f4vKwlQuR424g5OoAAAAAAAAJzA==

2013-11-21 | MSV000078497 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data