Gapped spectral dictionaries and their applications for database searches of tandem mass spectra (Q35026856)

5 August 2017

Gapped spectral dictionaries and their applications for database searches of tandem mass spectra (English)

1 reference

5 August 2017

4

Pavel A Pevzner

1 reference

5 August 2017

3

Nuno Bandeira

1 reference

5 August 2017

Kyowon Jeong

1

1 reference

PubMed ID

21444829

5 August 2017

Sangtae Kim

series ordinal

2

1 reference

5 August 2017

28 March 2011

1 reference

Molecular & Cellular Proteomics

5 August 2017

1 reference

5 August 2017

10

1 reference

5 August 2017

6

1 reference

5 August 2017

M110.002220

1 reference

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

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

A ranking-based scoring function for peptide-spectrum matches

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Discovery and revision of Arabidopsis genes by proteogenomics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Clustering millions of tandem mass spectra

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Improving gene annotation using peptide mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

PepNovo: de novo peptide sequencing via probabilistic network modeling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Open mass spectrometry search algorithm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Parallel identification of new genes in Saccharomyces cerevisiae

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Interrogating the human genome using uninterpreted mass spectrometry data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Mass spectrometry allows direct identification of proteins in large genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Functional assignment of the 20 S proteasome from Trypanosoma brucei using mass spectrometry and new bioinformatics approaches.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

De novo peptide sequencing via tandem mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3108828

Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry

25 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21444829

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21444829

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21444829

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1074/MCP.M110.002220

1 reference

5 August 2017

1 reference

5 August 2017

1 reference

PubMed ID

21444829