PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data (Q30836712)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25028575%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

title

PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data (English)

1 reference

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9 March 2020

0 references

4

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9 March 2020

Tuula A. Nyman

5

1 reference

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9 March 2020

Sandra Söderholm

1

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9 March 2020

Tiina Öhman

3

1 reference

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9 March 2020

author name string

Petteri Hintsanen

2

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9 March 2020

publication date

26 June 2014

1 reference

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9 March 2020

1 reference

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9 March 2020

volume

12

1 reference

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9 March 2020

page(s)

36

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describes a project that uses

9 March 2020

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Label-free quantitative phosphoproteomic analysis reveals differentially regulated proteins and pathway in PRRSV-infected pulmonary alveolar macrophages

1 reference

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

21 June 2018

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Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry

21 June 2018

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The N-terminal region of the DNA-dependent protein kinase catalytic subunit is required for its DNA double-stranded break-mediated activation

21 June 2018

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The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

21 June 2018

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Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics.

21 June 2018

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ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses

21 June 2018

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Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages

21 June 2018

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Andromeda: a peptide search engine integrated into the MaxQuant environment

21 June 2018

1 reference

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Reverse-phase phosphoproteome analysis of signaling pathways induced by Rift valley fever virus in human small airway epithelial cells

21 June 2018

1 reference

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Confident phosphorylation site localization using the Mascot Delta Score

21 June 2018

1 reference

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Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

ArMone: a software suite specially designed for processing and analysis of phosphoproteome data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes.

21 June 2018

1 reference

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PeptideDepot: flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information

21 June 2018

1 reference

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The phosphoproteomics data explosion.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

RIG-I-mediated activation of p38 MAPK is essential for viral induction of interferon and activation of dendritic cells: dependence on TRAF2 and TAK1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

KEA: kinase enrichment analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Structure and regulation of MARK, a kinase involved in abnormal phosphorylation of Tau protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Open mass spectrometry search algorithm

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

TANDEM: matching proteins with tandem mass spectra

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Expression and function of chemokines during viral infections: from molecular mechanisms to in vivo function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Protein kinase C beta (PKC beta): normal functions and diseases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Probability-based protein identification by searching sequence databases using mass spectrometry data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

PhosphoSiteAnalyzer: a bioinformatic platform for deciphering phospho proteomes using kinase predictions retrieved from NetworKIN.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

Universal and confident phosphorylation site localization using phosphoRS.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4098950

25 November 2018

Identifiers

DOI

10.1186/1477-5956-12-36

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25028575%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

9 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25028575%20AND%20SRC:MED&resulttype=core&format=json

9 March 2020

PubMed publication ID

25028575

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25028575%20AND%20SRC:MED&resulttype=core&format=json