Integrating shotgun proteomics and mRNA expression data to improve protein identification (Q33421651)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19318424%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

title

Integrating shotgun proteomics and mRNA expression data to improve protein identification (English)

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24 January 2020

3

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24 January 2020

Luiz O. F. Penalva

5

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24 January 2020

Edward Marcotte

7

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24 January 2020

author name string

Smriti R Ramakrishnan

1

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24 January 2020

Zhihua Li

4

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24 January 2020

Margaret Myers

6

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24 January 2020

Daniel P Miranker

8

1 reference

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24 January 2020

Rong Wang

9

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24 January 2020

Christine Vogel

2

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24 January 2020

language of work or name

English

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publication date

24 March 2009

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24 January 2020

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24 January 2020

volume

25

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24 January 2020

issue

11

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24 January 2020

page(s)

1397-1403

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Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

24 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Modes of inference for evaluating the confidence of peptide identifications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

A high-quality catalog of the Drosophila melanogaster proteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Expanded protein information at SGD: new pages and proteome browser.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Global analysis of protein phosphorylation in yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Integrating high-throughput and computational data elucidates bacterial networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

A combined transmembrane topology and signal peptide prediction method

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Characterizing gene sets with FuncAssociate

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

A statistical model for identifying proteins by tandem mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Comparing protein abundance and mRNA expression levels on a genomic scale

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Toward a protein profile of Escherichia coli: comparison to its transcription profile

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

A sampling of the yeast proteome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Dissecting the regulatory circuitry of a eukaryotic genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

Serial analysis of gene expression

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2682515

An introduction to ROC analysis

28 July 2018

1 reference

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Yeast phenotypic assays on translational control.

21 January 2018

1 reference

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Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.

21 January 2018

1 reference

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FunSpec: a web-based cluster interpreter for yeast

21 January 2018

1 reference

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Precision and functional specificity in mRNA decay

21 January 2018

1 reference

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Large-scale analysis of the yeast proteome by multidimensional protein identification technology

21 January 2018

1 reference

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Stable isotope labeling by amino acids in cell culture (SILAC) and proteome quantitation of mouse embryonic stem cells to a depth of 5,111 proteins

21 January 2018

1 reference

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10.1093/BIOINFORMATICS/BTP168

31 October 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19318424%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/RamakrishnanVPWLPMMM09

24 January 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19318424%20AND%20SRC:MED&resulttype=core&format=json

24 January 2020

1 reference