Template proteogenomics: sequencing whole proteins using an imperfect database (Q33883042)

29 July 2017

title

Template proteogenomics: sequencing whole proteins using an imperfect database (English)

1 reference

29 July 2017

0 references

Vineet Bafna

5

0 references

author name string

Natalie E Castellana

1

1 reference

29 July 2017

Victoria Pham

2

1 reference

29 July 2017

David Arnott

3

1 reference

29 July 2017

Jennie R Lill

4

1 reference

29 July 2017

publication date

17 February 2010

1 reference

Molecular & Cellular Proteomics

29 July 2017

published in

1 reference

29 July 2017

volume

9

1 reference

29 July 2017

issue

6

1 reference

29 July 2017

page(s)

1260-1270

1 reference

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

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=2877985

Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Discovery and revision of Arabidopsis genes by proteogenomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Automated de novo protein sequencing of monoclonal antibodies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Clustering millions of tandem 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=2877985

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Improving gene annotation using peptide 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=2877985

Novel gene and gene model detection using a whole genome open reading frame analysis in 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=2877985

Identification of post-translational modifications by blind search of 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=2877985

PepNovo: de novo peptide sequencing via probabilistic network modeling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Detection of large-scale variation in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Large-scale copy number polymorphism in the human genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

PEAKS: powerful software for peptide de novo sequencing 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=2877985

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

The Sequence of the Human Genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

Probability-based protein identification by searching sequence databases using 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=2877985

De novo peptide sequencing via 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=2877985

Antibody-antigen interactions: contact analysis and binding site topography.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

dbEST--database for "expressed sequence tags"

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877985

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

5 July 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

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.M900504-MCP200

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

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.M900504-MCP200

Mutation-tolerant protein identification by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

PepHMM: a hidden Markov model based scoring function for mass spectrometry database search.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

Error bounds for convolutional codes and an asymptotically optimum decoding algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

IMGT, the international ImMunoGeneTics database

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M900504-MCP200

Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20164058

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1074/MCP.M900504-MCP200

1 reference

29 July 2017

1 reference

29 July 2017

1 reference