Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy (Q38794889)

6 September 2017

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy (English)

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6 September 2017

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10 June 2020

author name string

Michael R Shortreed

2

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10 June 2020

Gloria M Sheynkman

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10 June 2020

Brian L Frey

4

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10 June 2020

Lloyd M Smith

5

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10 June 2020

publication date

25 December 2015

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Journal of Proteome Research

6 September 2017

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10 June 2020

volume

15

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10 June 2020

issue

3

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10 June 2020

page(s)

800-808

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Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search

10 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

6 September 2017

1 reference

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Proteogenomics: concepts, applications and computational strategies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

A pan-cancer proteomic perspective on The Cancer Genome Atlas.

6 September 2017

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Statistical Modeling of RNA-Seq Data.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

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

6 September 2017

1 reference

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Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

False discovery rates in spectral identification

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

De novo derivation of proteomes from transcriptomes for transcript and protein identification

6 September 2017

1 reference

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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

A bioinformatics workflow for variant peptide detection in shotgun proteomics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Posttranslational modification of p53: cooperative integrators of function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Galaxy: a web-based genome analysis tool for experimentalists

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

CanProVar: a human cancer proteome variation database

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

TopHat: discovering splice junctions with RNA-Seq

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Posterior error probabilities and false discovery rates: two sides of the same coin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Galaxy: a platform for interactive large-scale genome analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

SnapShot: histone modifications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4779408

10.1021/ACS.JPROTEOME.5B00817

31 August 2018

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26704769%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

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10 June 2020

PubMed publication ID

26704769

1 reference