Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics

(2017) Fredrik Boulund et al.   MOLECULAR & CELLULAR PROTEOMICS

Evaluation of different peptide fragmentation types and mass analyzers in data-dependent methods using an Orbitrap Fusion Lumos Tribrid mass spectrometer

(2017) Guadalupe Espadas et al.   PROTEOMICS

Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution

(2016) Gelio Alves et al.   BIOINFORMATICS

A comprehensive and scalable database search system for metaproteomics

(2016) Sandip Chatterjee et al.   BMC GENOMICS

The impact of sequence database choice on metaproteomic results in gut microbiota studies

(2016) Alessandro Tanca et al.   Microbiome

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

(2016) Xu Zhang et al.   Microbiome

Evolution of Orbitrap Mass Spectrometry Instrumentation

(2015) Shannon Eliuk et al.   Annual Review of Analytical Chemistry

Emerging methodologies for pathogen identification in positive blood culture testing

(2015) Grégory Dubourg et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

(2015) Gelio Alves et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Metaproteomic analysis using the Galaxy framework

(2015) Pratik D. Jagtap et al.   PROTEOMICS

Proteotyping: Proteomic characterization, classification and identification of microorganisms – A prospectus

(2015) Roger Karlsson et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Application of metagenomics in the human gut microbiome

(2015) Wei-Lin Wang et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research

(2015) Brendan P. Hodkinson et al.   Advances in Wound Care

Mass spectrometry-based protein identification with accurate statistical significance assignment

(2014) Gelio Alves et al.   BIOINFORMATICS

Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics

(2014) Anke Penzlin et al.   BIOINFORMATICS

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

(2014) Allyson L Byrd et al.   BMC BIOINFORMATICS

Rapid Identification of Microorganisms from Sterile Body Fluids by Use of FilmArray

(2014) Osman Altun et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Evaluation of FilmArray and Verigene Systems for Rapid Identification of Positive Blood Cultures: TABLE 1

(2014) M. M. Bhatti et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Rapid detection of single bacteria in unprocessed blood using Integrated Comprehensive Droplet Digital Detection

(2014) Dong-Ku Kang et al.   Nature Communications

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

A simple shotgun proteomics method for rapid bacterial identification

(2013) Dobryan M. Tracz et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space

(2013) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Strain-Level Typing and Identification of Bacteria Using Mass Spectrometry-Based Proteomics

(2012) Roger Karlsson et al.   JOURNAL OF PROTEOME RESEARCH

Unipept: Tryptic Peptide-Based Biodiversity Analysis of Metaproteome Samples

(2012) Bart Mesuere et al.   JOURNAL OF PROTEOME RESEARCH

Genome sequencing in clinical microbiology

(2012) Jacqueline Z-M Chan et al.   NATURE BIOTECHNOLOGY

Transforming clinical microbiology with bacterial genome sequencing

(2012) Xavier Didelot et al.   NATURE REVIEWS GENETICS

Novel Electrical Method for Early Detection of Viable Bacteria in Blood Cultures

(2011) Sachidevi Puttaswamy et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Comment on “Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies”

(2011) Marshall Bern et al.   JOURNAL OF PROTEOME RESEARCH

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

(2011) Gelio Alves et al.   PLoS One

Double-Blind Characterization of Non-Genome-Sequenced Bacteria by Mass Spectrometry-Based Proteomics

(2010) R. E. Jabbour et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Robust and accurate data enrichment statistics via distribution function of sum of weights

(2010) Aleksandar Stojmirović et al.   BIOINFORMATICS

Metagenomics: Facts and Artifacts, and Computational Challenges

(2010) John C. Wooley et al.   JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY

A Protein Processing Filter Method for Bacterial Identification by Mass Spectrometry-Based Proteomics

(2010) Rabih E. Jabbour et al.   JOURNAL OF PROTEOME RESEARCH

Data maximization by multipass analysis of protein mass spectra

(2010) Ravi Tharakan et al.   PROTEOMICS

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Rapid Identification of Bacteria in Positive Blood Culture Broths by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

(2009) L. G. Stevenson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mass spectrometry tools for the classification and identification of bacteria

(2009) Sascha Sauer et al.   NATURE REVIEWS MICROBIOLOGY

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota

(2009) Lance B. Price et al.   PLoS One

Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

(2008) Guanghui Wang et al.   ANALYTICAL CHEMISTRY

Enhancing Peptide Identification Confidence by Combining Search Methods

(2008) Gelio Alves et al.   JOURNAL OF PROTEOME RESEARCH