Computational and statistical analysis of protein mass spectrometry data (Q34145620)

31 July 2017

2 references

19 September 2019

8 April 2021

Computational and statistical analysis of protein mass spectrometry data (English)

1 reference

biomedical investigative technique

31 July 2017

0 references

1 reference

PubMed

19 September 2019

computational biology

2 references

8 April 2021

1

William Stafford Noble

1 reference

31 July 2017

2

Michael J MacCoss

1 reference

31 July 2017

publication date

26 January 2012

1 reference

PLOS Computational Biology

31 July 2017

1 January 2012

2 references

19 September 2019

8 April 2021

3 references

31 July 2017

19 September 2019

8 April 2021

8

1 reference

31 July 2017

issue

1

1 reference

31 July 2017

page(s)

e1002296

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

copyright license

2 references

19 September 2019

Assigning spectrum-specific P-values to protein identifications by mass spectrometry

8 April 2021

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Faster, Quantitative, and Accurate Precursor Acquisition Independent From Ion Count

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to 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=3266873

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

The 20S proteasome splicing activity discovered by SpliceMet

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

On the zwitterionic nature of gas-phase peptides and protein ions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Label-free, normalized quantification of complex mass spectrometry data for proteomic 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=3266873

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Statistical calibration of the SEQUEST XCorr function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Stable isotopic labeling in proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Decision tree-driven tandem mass spectrometry for shotgun proteomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Selected reaction monitoring for quantitative proteomics: a tutorial

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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=3266873

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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=3266873

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Quantification of proteins and metabolites by mass spectrometry without isotopic labeling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Absolute quantification strategies in proteomics based on mass spectrometry.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Ion activation methods for tandem mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

A statistical model for identifying proteins by tandem mass spectrometry

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3266873

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=3266873

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

28 July 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

A statistical framework for protein quantitation in bottom-up MS-based proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Computational prediction of proteotypic peptides for quantitative proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Scoring proteomes with proteotypic peptide probes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002296

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22291580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein quantification in label-free LC-MS experiments

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22291580

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1002296

1 reference

31 July 2017

DBLP publication ID

journals/ploscb/NobleM12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

31 July 2017

1 reference