Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis (Q33832543)

29 July 2017

Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis (English)

1 reference

29 July 2017

Alexey I. Nesvizhskii

object named as

Alexey I Nesvizhskii

4

0 references

author name string

Damian Fermin

1

1 reference

PubMed ID

21360675

29 July 2017

Venkatesha Basrur

2

1 reference

PubMed ID

21360675

29 July 2017

Anastasia K Yocum

3

1 reference

29 July 2017

17 February 2011

1 reference

29 July 2017

1 reference

29 July 2017

11

1 reference

29 July 2017

7

1 reference

29 July 2017

1340-1345

1 reference

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Protein and gene model inference based on statistical modeling in k-partite graphs.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

A global protein kinase and phosphatase interaction network in yeast.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

PepC: proteomics software for identifying differentially expressed proteins based on spectral counting

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

In-depth proteomic analyses of direct expressed prostatic secretions

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Role of spectral counting in quantitative proteomics.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

A guided tour of the Trans-Proteomic Pipeline

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

ReSASC: a resampling-based algorithm to determine differential protein expression from spectral count data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

RNA-Seq gene expression estimation with read mapping uncertainty

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Current trends in quantitative proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Mass spectrometry-based label-free quantitative proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Network-assisted protein identification and data interpretation in shotgun proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

A bayesian approach to protein inference problem in shotgun proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Estimating accuracy of RNA-Seq and microarrays with proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Statistical inferences for isoform expression in RNA-Seq

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Significance analysis of spectral count data in label-free shotgun proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

PatternLab for proteomics: a tool for differential shotgun proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Sorting signals, N-terminal modifications and abundance of the chloroplast proteome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Interpretation of shotgun proteomic data: the protein inference problem

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

A statistical model for identifying proteins by tandem mass spectrometry

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3113614

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

4 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPMIC.201000650

Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPMIC.201000650

Statistical Analysis of Membrane Proteome Expression Changes inSaccharomycescerevisiae

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPMIC.201000650

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21360675

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PMIC.201000650

1 reference

29 July 2017

1 reference

29 July 2017

1 reference

PubMed ID

21360675