Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

Chemoproteomics Reveals Time-Dependent Binding of Histone Deacetylase Inhibitors to Endogenous Repressor Complexes

(2014) Isabelle Becher et al.   ACS Chemical Biology

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

Ion Coalescence of Neutron Encoded TMT 10-Plex Reporter Ions

(2014) Thilo Werner et al.   ANALYTICAL CHEMISTRY

Polypharmacology: Challenges and Opportunities in Drug Discovery

(2014) Andrew Anighoro et al.   JOURNAL OF MEDICINAL CHEMISTRY

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

(2014) Navin Rauniyar et al.   JOURNAL OF PROTEOME RESEARCH

NQO2 Is a Reactive Oxygen Species Generating Off-Target for Acetaminophen

(2014) Teemu P. Miettinen et al.   MOLECULAR PHARMACEUTICS

The cellular thermal shift assay for evaluating drug target interactions in cells

(2014) Rozbeh Jafari et al.   Nature Protocols

Phenotypic screening in cancer drug discovery — past, present and future

(2014) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

Tracking cancer drugs in living cells by thermal profiling of the proteome

(2014) M. M. Savitski et al.   SCIENCE

Reducing attrition in drug development: smart loading preclinical safety assessment

(2013) Ruth A. Roberts et al.   DRUG DISCOVERY TODAY

Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification

(2013) Mikhail M. Savitski et al.   JOURNAL OF PROTEOME RESEARCH

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Tracking Drugs

(2013) Jing Huang   NEW ENGLAND JOURNAL OF MEDICINE

Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay

(2013) D. M. Molina et al.   SCIENCE

Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell

(2013) Ignacio Asial et al.   Nature Communications

Affinity Profiling of the Cellular Kinome for the Nucleotide Cofactors ATP, ADP, and GTP

(2012) Isabelle Becher et al.   ACS Chemical Biology

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

High-Resolution Enabled TMT 8-plexing

(2012) Thilo Werner et al.   ANALYTICAL CHEMISTRY

Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients

(2012) Thomas Köcher et al.   Nature Protocols

On the origins of drug polypharmacology

(2012) Xavier Jalencas et al.   MedChemComm

Delayed Fragmentation and Optimized Isolation Width Settings for Improvement of Protein Identification and Accuracy of Isobaric Mass Tag Quantification on Orbitrap-Type Mass Spectrometers

(2011) Mikhail M. Savitski et al.   ANALYTICAL CHEMISTRY

thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome DiscoverermsfFiles

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

(2011) Annette Michalski et al.   MOLECULAR & CELLULAR PROTEOMICS

mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets

(2011) Mathias Wilhelm et al.   MOLECULAR & CELLULAR PROTEOMICS

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

(2011) Marcus Bantscheff et al.   NATURE BIOTECHNOLOGY

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

H-Score, a Mass Accuracy Driven Rescoring Approach for Improved Peptide Identification in Modification Rich Samples

(2010) Mikhail M Savitski et al.   JOURNAL OF PROTEOME RESEARCH

Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays

(2010) Mikhail M. Savitski et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Chemoproteomics-based kinome profiling and target deconvolution of clinical multi-kinase inhibitors in primary chronic lymphocytic leukemia cells

(2010) U Kruse et al.   LEUKEMIA

Simultaneous analysis of relative protein expression levels across multiple samples using iTRAQ isobaric tags with 2D nano LC–MS/MS

(2010) Richard D Unwin et al.   Nature Protocols

Histone deacetylase inhibitors: A new mode for inhibition of cholesterol metabolism

(2009) Sridar V Chittur et al.   BMC GENOMICS

Development of the pan-DAC inhibitor panobinostat (LBH589): Successes and challenges

(2009) Peter Atadja   CANCER LETTERS

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

(2009) Jürgen Cox et al.   Nature Protocols

Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags

(2008) Loïc Dayon et al.   ANALYTICAL CHEMISTRY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY