(Q36268706)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

title

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

0 references

Honglan Li

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

Yoon Sung Joh

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

Sang-Won Lee

series ordinal

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

Kyu-Baek Hwang

series ordinal

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

language of work or name

English

0 references

publication date

22 December 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

issue

Suppl 13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

page(s)

1031

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

Proteogenomics: concepts, applications and computational strategies

9 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomic characterization of human colon and rectal cancer

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

A draft map of the human proteome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Identification of gene fusions from human lung cancer mass spectrometry data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Database construction and peptide identification strategies for proteogenomic studies on sequenced genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomic database construction driven from large scale RNA-seq data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Comet: an open-source MS/MS sequence database search tool

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomics to discover the full coding content of genomes: a computational perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Discovery and revision of Arabidopsis genes by proteogenomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

The UniProtKB/Swiss-Prot knowledgebase and its plant proteome annotation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

RNA-Seq: a revolutionary tool for transcriptomics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomics: needs and roles to be filled by proteomics in genome annotation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Improving gene annotation using peptide mass spectrometry

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Multidimensional protein identification technology (MudPIT): technical overview of a profiling method optimized for the comprehensive proteomic investigation of normal and diseased heart tissue

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

TANDEM: matching proteins with tandem mass spectra

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Proteogenomic mapping as a complementary method to perform genome annotation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Improving X!Tandem on peptide identification from mass spectrometry by self-boosted Percolator.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5259817

Target-Decoy with Mass Binning: a simple and effective validation method for shotgun proteomics using high resolution mass spectrometry

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28155652

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12864-016-3327-5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28155652%20AND%20SRC:MED&resulttype=core&format=json

9 April 2020

PubMed publication ID

28155652

1 reference