Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics (Q37097028)

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scientific article published on 13 September 2008

Language	Label	Description	Also known as
English	Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics	scientific article published on 13 September 2008

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics (English)

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

0 references

Shotgun proteomics

1 reference

based on heuristic

inferred from title

object named as

Ying Ding

1

0 references

object named as

Hyungwon Choi

2

0 references

Alexey I. Nesvizhskii

object named as

Alexey I Nesvizhskii

3

0 references

publication date

13 September 2008

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Journal of Proteome Research

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

7

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

11

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

4878-4889

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

1 reference

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29 September 2017

Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Modes of inference for evaluating the confidence of peptide identifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Posterior error probabilities and false discovery rates: two sides of the same coin

1 reference

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29 September 2017

Analysis and validation of proteomic data generated by tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

On the proper use of mass accuracy in proteomics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Bioinformatic methods to exploit mass spectrometric data for proteomic applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Large scale analysis of MASCOT results using a Mass Accuracy-based THreshold (MATH) effectively improves data interpretation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Interpretation of shotgun proteomic data: the protein inference problem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. New developments in Protein Prospector allow for reliab

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

The ABC's (and XYZ's) of peptide sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

TANDEM: matching proteins with tandem mass spectra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

A statistical model for identifying proteins by tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Mass spectrometry-based proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

29 September 2017

Properties of average score distributions of SEQUEST: the probability ratio method.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

EBP, a program for protein identification using multiple tandem mass spectrometry datasets.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

Optimization and use of peptide mass measurement accuracy in shotgun proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

Trypsin cleaves exclusively C-terminal to arginine and lysine residues

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

3 September 2018

Head-to-Head Comparison of Serum Fractionation Techniques

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3744223

4 December 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/18788775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The implications of proteolytic background for shotgun proteomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/18788775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/PR800484X

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

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