IsoformResolver: A peptide-centric algorithm for protein inference. (Q38314494)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21599010%20AND%20SRC:MED&resulttype=core&format=json

1 February 2020

title

IsoformResolver: A peptide-centric algorithm for protein inference (English)

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1 February 2020

2

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1 February 2020

author name string

Karen Meyer-Arendt

1

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1 February 2020

Stephane Houel

3

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1 February 2020

Kutralanathan Renganathan

4

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1 February 2020

Brian Eichelberger

5

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1 February 2020

Katheryn A Resing

6

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1 February 2020

Natalie G Ahn

7

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1 February 2020

publication date

7 June 2011

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Journal of Proteome Research

1 February 2020

published in

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1 February 2020

volume

10

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1 February 2020

issue

7

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1 February 2020

page(s)

3060-3075

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

1 February 2020

cites work

1 reference

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Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies.

6 September 2017

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Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets

6 September 2017

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

6 September 2017

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Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma

6 September 2017

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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

6 September 2017

1 reference

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BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

6 September 2017

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Distinguishing protein-coding and noncoding genes in the human genome

6 September 2017

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The minimum information about a proteomics experiment (MIAPE)

6 September 2017

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Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Probability model for assessing proteins assembled from peptide sequences inferred from tandem mass spectrometry 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=3167374

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=3167374

Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS 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=3167374

Interpretation of shotgun proteomic data: the protein inference problem

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

DBParser: web-based software for shotgun proteomic data analyses

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

The International Protein Index: an integrated database for proteomics experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in 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=3167374

A statistical model for identifying proteins by tandem 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=3167374

DTASelect and Contrast: tools for assembling and comparing protein identifications from 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=3167374

What does it mean to identify a protein in 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=3167374

Probability-based protein identification by searching sequence databases using mass spectrometry 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=3167374

Improving reproducibility and sensitivity in identifying human proteins by 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=3167374

The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Improved validation of peptide MS/MS assignments using spectral intensity prediction.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Reporting protein identification data: the next generation of guidelines.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

Prediction of low-energy collision-induced dissociation spectra of peptides

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167374

In vitro and in silico processes to identify differentially expressed proteins

31 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21599010

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/PR200039P

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21599010%20AND%20SRC:MED&resulttype=core&format=json

1 February 2020

1 reference

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1 February 2020

PubMed publication ID

21599010

1 reference