Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

(2012) Hannes Röst et al.   MOLECULAR & CELLULAR PROTEOMICS

Software for Quantitative Proteomic Analysis Using Stable Isotope Labeling and Data Independent Acquisition

(2011) Xin Huang et al.   ANALYTICAL CHEMISTRY

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

(2011) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600)

(2011) Genna L. Andrews et al.   ANALYTICAL CHEMISTRY

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC−MS/MS

(2011) Annette Michalski et al.   JOURNAL OF PROTEOME RESEARCH

mProphet: automated data processing and statistical validation for large-scale SRM experiments

(2011) Lukas Reiter et al.   NATURE METHODS

Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer

(2011) I. Cima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and identification of 700 drugs by multi-target screening with a 3200 Q TRAP® LC-MS/MS system and library searching

(2010) S. Dresen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Advances in Mass Spectrometry for Lipidomics

(2010) Stephen J. Blanksby et al.   Annual Review of Analytical Chemistry

XDIA: improving on the label-free data-independent analysis

(2010) Paulo C. Carvalho et al.   BIOINFORMATICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Mass spectrometry–based proteomics in cell biology

(2010) Tobias C. Walther et al.   JOURNAL OF CELL BIOLOGY

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

Improving Protein and Proteome Coverage through Data-Independent Multiplexed Peptide Fragmentation

(2010) Kevin Blackburn et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics on an Orbitrap Benchtop Mass Spectrometer Using All-ion Fragmentation

(2010) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

ESI-MS/MS library of 1,253 compounds for application in forensic and clinical toxicology

(2009) Sebastian Dresen et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Precursor Acquisition Independent From Ion Count: How to Dive Deeper into the Proteomics Ocean

(2009) Alexandre Panchaud et al.   ANALYTICAL CHEMISTRY

Deconvolution of Mixture Spectra from Ion-Trap Data-Independent-Acquisition Tandem Mass Spectrometry

(2009) Marshall Bern et al.   ANALYTICAL CHEMISTRY

ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics

(2009) Jason WH Wong et al.   BMC BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity

(2009) Jamie Sherman et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Quantifying proteins by mass spectrometry: The selectivity of SRM is only part of the problem

(2009) Mark W. Duncan et al.   PROTEOMICS

How specific is my SRM?: The issue of precursor and product ion redundancy

(2009) Jamie Sherman et al.   PROTEOMICS

Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

(2009) Guo-Zhong Li et al.   PROTEOMICS

The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS

(2009) Scott J. Geromanos et al.   PROTEOMICS

Mass spectrometry for proteomics

(2008) Xuemei Han et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

A database of mass spectrometric assays for the yeast proteome

(2008) Paola Picotti et al.   NATURE METHODS