A linear programming model for protein inference problem in shotgun proteomics

Protein inference: a review

(2012) T. Huang et al.   BRIEFINGS IN BIOINFORMATICS

Direct Maximization of Protein Identifications from Tandem Mass Spectra

(2011) Marina Spivak et al.   MOLECULAR & CELLULAR PROTEOMICS

A nested mixture model for protein identification using mass spectrometry

(2010) Qunhua Li et al.   Annals of Applied Statistics

Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data

(2010) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

PeptideClassifier for protein inference and targeted quantitative proteomics

(2010) Ermir Qeli et al.   NATURE BIOTECHNOLOGY

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

(2010) S. Gerster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Brian C. Searle   PROTEOMICS

MassSieve: Panning MS/MS peptide data for proteins

(2010) Douglas J. Slotta et al.   PROTEOMICS

Integrating shotgun proteomics and mRNA expression data to improve protein identification

(2009) Smriti R. Ramakrishnan et al.   BIOINFORMATICS

Mining gene functional networks to improve mass-spectrometry-based protein identification

(2009) Smriti R. Ramakrishnan et al.   BIOINFORMATICS

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

(2009) M. A. Grobei et al.   GENOME RESEARCH

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

(2009) Yong Fuga Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering

(2009) Ze-Qiang Ma et al.   JOURNAL OF PROTEOME RESEARCH

Network-assisted protein identification and data interpretation in shotgun proteomics

(2009) Jing Li et al.   Molecular Systems Biology

Improving Protein Identification Sensitivity by Combining MS and MS/MS Information for Shotgun Proteomics Using LTQ-Orbitrap High Mass Accuracy Data

(2008) Bingwen Lu et al.   ANALYTICAL CHEMISTRY

Improved Ranking Functions for Protein and Modification-Site Identifications

(2008) Marshall Bern et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Protein Identification and Peptide Expression Resolver: Harmonizing Protein Identification with Protein Expression Data

(2007) Paul Kearney et al.   JOURNAL OF PROTEOME RESEARCH

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools

(2007) John Klimek et al.   JOURNAL OF PROTEOME RESEARCH