ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects (Q36240436)

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19 February 2020

title

ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects (English)

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19 February 2020

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19 February 2020

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19 February 2020

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19 February 2020

Tao Xu

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19 February 2020

Bing Shan

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19 February 2020

Aaron Aslanian

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19 February 2020

Xuemei Han

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19 February 2020

Nobel Zong

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19 February 2020

Haomin Li

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19 February 2020

Howard Choi

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19 February 2020

Dong Wang

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19 February 2020

Lipi Acharya

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19 February 2020

Lisa Du

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19 February 2020

Peipei Ping

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19 February 2020

John R Yates

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19 February 2020

publication date

18 July 2015

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19 February 2020

published in

Journal of Proteomics

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19 February 2020

volume

129

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19 February 2020

page(s)

25-32

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Mass-spectrometry-based draft of the human proteome

19 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

A draft map of the human proteome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Protein analysis by shotgun/bottom-up proteomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Dynamics of subcellular proteomes during brain development

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Search engine processor: Filtering and organizing peptide spectrum matches

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Generic comparison of protein inference engines

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Two-dimensional target decoy strategy for shotgun proteomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

IsoformResolver: A peptide-centric algorithm for protein inference.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Improved ranking functions for protein and modification-site identifications

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Interpretation of shotgun proteomic data: the protein inference problem

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

A statistical model for identifying proteins by tandem mass spectrometry

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

Shotgun protein identification and quantification by mass spectrometry.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630118

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

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26196237

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.JPROT.2015.07.006

1 reference

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19 February 2020

1 reference

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19 February 2020

PubMed publication ID

26196237

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26196237%20AND%20SRC:MED&resulttype=core&format=json