A nonparametric model for quality control of database search results in shotgun proteomics (Q33315484)

25 July 2017

A nonparametric model for quality control of database search results in shotgun proteomics (English)

1 reference

25 July 2017

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Jiyang Zhang

1

1 reference

25 July 2017

Jianqi Li

2

1 reference

25 July 2017

Xin Liu

3

1 reference

25 July 2017

Hongwei Xie

4

1 reference

25 July 2017

Yunping Zhu

5

1 reference

25 July 2017

Fuchu He

6

1 reference

25 July 2017

21 January 2008

1 reference

25 July 2017

1 reference

25 July 2017

9

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25 July 2017

29

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2105-9-29

25 July 2017

0 references

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

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A new strategy to filter out false positive identifications of peptides in SEQUEST database search results

14 July 2018

1 reference

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Analysis of human liver proteome using replicate shotgun strategy

14 July 2018

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A probability-based approach for high-throughput protein phosphorylation analysis and site localization

14 July 2018

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The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins

14 July 2018

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Challenges and opportunities in proteomics data analysis

14 July 2018

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Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system

14 July 2018

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Large-scale and high-confidence proteomic analysis of human seminal plasma

14 July 2018

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Mass spectrometry and protein analysis

14 July 2018

1 reference

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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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Improved classification of mass spectrometry database search results using newer machine learning approaches

14 July 2018

1 reference

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Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations

14 July 2018

1 reference

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Computational cluster validation in post-genomic data analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Nucleolar proteome dynamics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

DBParser: web-based software for shotgun proteomic data analyses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

RScore: a peptide randomicity score for evaluating tandem mass spectra

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Standard mixtures for proteome studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome

14 July 2018

1 reference

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DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Mass spectrometry-based proteomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Proteomics: the first decade and beyond

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Proteomics to study genes and genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Direct analysis of protein complexes using mass spectrometry

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Improved validation of peptide MS/MS assignments using spectral intensity prediction.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Optimization and use of peptide mass measurement accuracy in shotgun proteomics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Randomized sequence databases for tandem mass spectrometry peptide and protein identification.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Valid data from large-scale proteomics studies.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

The need for a public proteomics repository.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Artificial neural network analysis for evaluation of peptide MS/MS spectra in proteomics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics: Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Qscore: an algorithm for evaluating SEQUEST database search results

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2267700

Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18205957

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18205957

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-9-29

1 reference

journals/bmcbi/ZhangLLXZH08

25 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

25 July 2017

1 reference