Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS). (Q36089853)

12 August 2017

Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS). (English)

1 reference

12 August 2017

5

Dominic Winter

1 reference

12 August 2017

Bernhard Y Renard

1

0 references

author name string

Buote Xu

2

1 reference

12 August 2017

Marc Kirchner

3

1 reference

12 August 2017

Franziska Zickmann

4

1 reference

12 August 2017

Simone Korten

6

1 reference

12 August 2017

Norbert W Brattig

7

1 reference

12 August 2017

Amit Tzur

8

1 reference

12 August 2017

Fred A Hamprecht

9

1 reference

12 August 2017

Hanno Steen

10

1 reference

12 August 2017

6 April 2012

1 reference

Molecular & Cellular Proteomics

12 August 2017

1 reference

12 August 2017

11

1 reference

12 August 2017

7

1 reference

12 August 2017

M111.014167

1 reference

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

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

A bioinformatics workflow for variant peptide detection in shotgun proteomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

TagRecon: high-throughput mutation identification through sequence tagging

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Cross species proteomics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Tools for exploring the proteomosphere

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Automated de novo protein sequencing of monoclonal antibodies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Computational methods for protein identification from mass spectrometry data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Analysis and validation of proteomic data generated by tandem mass spectrometry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Virtual polymorphism: finding divergent peptide matches in mass spectrometry data.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

PepNovo: de novo peptide sequencing via probabilistic network modeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

TANDEM: matching proteins with tandem mass spectra

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

The power and the limitations of cross-species protein identification by mass spectrometry-driven sequence similarity searches

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Error tolerant searching of uninterpreted tandem mass spectrometry data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Litomosoides sigmodontis in mice: reappraisal of an old model for filarial research

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

A molecular evolutionary framework for the phylum Nematoda

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Error-tolerant identification of peptides in sequence databases by peptide sequence tags

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Protein identification pipeline for the homology-driven proteomics.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394943

Error-tolerant EST database searches by tandem mass spectrometry and multiTag software.

11 July 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

Peptide sequence tag-based blind identification of post-translational modifications with point process model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M111.014167

A method for reducing the time required to match protein sequences with tandem mass spectra

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22493179

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Estimating the confidence of peptide identifications without decoy databases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22493179

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A workflow to increase the detection rate of proteins from unsequenced organisms in high-throughput proteomics experiments

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22493179

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1074/MCP.M111.014167

1 reference

12 August 2017

1 reference

12 August 2017

1 reference