(Q33777108)

29 July 2017

title

On the accuracy and limits of peptide fragmentation spectrum prediction (English)

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29 July 2017

4

Predrag Radivojac

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29 July 2017

Sujun Li

1

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29 July 2017

Randy J Arnold

series ordinal

2

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29 July 2017

Haixu Tang

series ordinal

3

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29 July 2017

language of work or name

English

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publication date

22 December 2010

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29 July 2017

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29 July 2017

volume

83

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29 July 2017

issue

3

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29 July 2017

page(s)

790-796

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The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics

29 July 2017

cites work

1 reference

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28 July 2018

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Predicting intensity ranks of peptide fragment ions

28 July 2018

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A simple workflow to increase MS2 identification rate by subsequent spectral library search

28 July 2018

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Building consensus spectral libraries for peptide identification in proteomics

28 July 2018

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Review of factors that influence the abundance of ions produced in a tandem mass spectrometer and statistical methods for discovering these factors

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Clustering millions of tandem mass spectra

28 July 2018

1 reference

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A platform for accurate mass and time analyses of mass spectrometry data

28 July 2018

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Development and validation of a spectral library searching method for peptide identification from MS/MS.

28 July 2018

1 reference

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MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

28 July 2018

1 reference

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Methods for peptide identification by spectral comparison

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Using annotated peptide mass spectrum libraries for protein identification

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns

28 July 2018

1 reference

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The use of proteotypic peptide libraries for protein identification

28 July 2018

1 reference

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Informatics for protein identification by mass spectrometry

28 July 2018

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28 July 2018

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Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

28 July 2018

1 reference

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Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

The critical evaluation of a comprehensive mass spectral library

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Emerging tandem-mass-spectrometry techniques for the rapid identification of proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

A machine learning approach to predicting peptide fragmentation spectra.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

A computational approach toward label-free protein quantification using predicted peptide detectability.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Central limit theorem as an approximation for intensity-based scoring function

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Scoring proteomes with proteotypic peptide probes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Prediction of low-energy collision-induced dissociation spectra of peptides

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Impact of ion trap tandem mass spectra variability on the identification of peptides.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

Intensity-based protein identification by machine learning from a library of tandem mass spectra.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3036742

30 October 2018

Identifiers

DOI

10.1021/AC102272R

1 reference

29 July 2017

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29 July 2017

1 reference