(Q26999422)

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Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments

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Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments (English)

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author name string

I. M. Armean

1

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K. S. Lilley

2

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M. W. B. Trotter

3

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language of work or name

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publication date

January 2013

1 reference

Molecular & Cellular Proteomics

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12

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1

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1-13

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28 September 2017

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28 September 2017

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28 September 2017

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28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Global networks of functional coupling in eukaryotes from comprehensive data integration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Literature-curated protein interaction datasets.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

An experimentally derived confidence score for binary protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Evolution of genome architecture

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Challenges and rewards of interaction proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Mapping multiprotein complexes by affinity purification and mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

TiGER: a database for tissue-specific gene expression and regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Next-generation high-density self-assembling functional protein arrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Analysis and validation of proteomic data generated by tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Literature-based concept profiles for gene annotation: the issue of weighting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

The minimum information required for reporting a molecular interaction experiment (MIMIx).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Deciphering protein-protein interactions. Part I. Experimental techniques and databases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Proteome chips for whole-organism assays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Choosing negative examples for the prediction of protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

High-throughput two-hybrid analysis. The promise and the peril

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Mechanism of divergent growth factor effects in mesenchymal stem cell differentiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Capturing protein interactions in the secretory pathway of living cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

A survey of current work in biomedical text mining

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

A novel strategy for quantitative proteomics using isotope-coded protein labels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

The evolutionary dynamics of eukaryotic gene order

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

FusionDB: a database for in-depth analysis of prokaryotic gene fusion events

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Protein families and TRIBES in genome sequence space

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

How reliable are experimental protein-protein interaction data?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Function prediction and protein networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

MAPPIT: a cytokine receptor-based two-hybrid method in mammalian cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Inferring domain-domain interactions from protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Protein interactions: two methods for assessment of the reliability of high throughput observations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

Modeling contaminants in AP-MS/MS experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 September 2017

COXPRESdb: a database to compare gene coexpression in seven model animals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

31 May 2018

The Negatome database: a reference set of non-interacting protein pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

31 May 2018

Up-to-date catalogues of yeast protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

31 May 2018

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

31 May 2018

Analyzing protein complexes in Drosophila with tandem affinity purification-mass spectrometry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

31 May 2018

The cell as a collection of protein machines: preparing the next generation of molecular biologists

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Exhaustive benchmarking of the yeast two-hybrid system.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

On lines and planes of closest fit to systems of points in space

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Using phylogenetic profiles to predict functional relationships.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Comparative analysis and unification of domain-domain interaction networks.

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Recurated protein interaction datasets

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Genome evolution

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Erratum: Addendum: Literature-curated protein interaction datasets

1 reference

https://api.crossref.org/works/10.1074%2FMCP.R112.019554

21 January 2018

Tandem immunoaffinity purification of protein complexes from Caenorhabditis elegans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3536891

28 November 2018

The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 study: relative protein quantitation

1 reference

https://pubmed.ncbi.nlm.nih.gov/23071097

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Quality control methodology for high-throughput protein-protein interaction screening

1 reference

https://pubmed.ncbi.nlm.nih.gov/23071097

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The study of macromolecular complexes by quantitative proteomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/23071097

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1074/MCP.R112.019554

0 references

PMC publication ID

1 reference

PubMed publication ID

1 reference

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