(Q33857415)

29 July 2017

title

Hierarchical clustering of shotgun proteomics data (English)

1 reference

29 July 2017

main subject

hierarchical clustering

1 reference

1 reference

Ville R Koskinen

1

1 reference

29 July 2017

Patrick A Emery

series ordinal

2

1 reference

29 July 2017

David M Creasy

series ordinal

3

1 reference

29 July 2017

John S Cottrell

series ordinal

4

1 reference

29 July 2017

publication date

29 March 2011

1 reference

Molecular & Cellular Proteomics

29 July 2017

published in

1 reference

29 July 2017

volume

10

1 reference

29 July 2017

issue

6

1 reference

29 July 2017

page(s)

M110.003822

1 reference

MassSieve: panning MS/MS peptide data for proteins

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Database resources of the National Center for Biotechnology Information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Network-assisted protein identification and data interpretation in shotgun proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

A bayesian approach to protein inference problem in shotgun proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

False discovery rates of protein identifications: a strike against the two-peptide rule

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Clustal W and Clustal X version 2.0

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Interpretation of shotgun proteomic data: the protein inference problem

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Scoring proteomes with proteotypic peptide probes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

A Heuristic method for assigning a false-discovery rate for protein identifications from Mascot database search results

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

DBParser: web-based software for shotgun proteomic data analyses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

A statistical model for identifying proteins by tandem mass spectrometry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

PRISM, a generic large scale proteomic investigation strategy for mammals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

EBP, a program for protein identification using multiple tandem mass spectrometry datasets.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Qscore: an algorithm for evaluating SEQUEST database search results

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108832

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21447708

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

PeptideClassifier for protein inference and targeted quantitative proteomics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21447708

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The pros and cons of peptide-centric proteomics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21447708

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1074/MCP.M110.003822

1 reference

29 July 2017

1 reference

29 July 2017

1 reference