Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Benchmarking common quantification strategies for large-scale phosphoproteomics

(2018) Alexander Hogrebe et al.   Nature Communications

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry

(2016) Sibylle Pfammatter et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status

(2016) F. Coscia et al.   Nature Communications

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

(2015) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis

(2015) Gitte Böhm et al.   JOURNAL OF PROTEOME RESEARCH

Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts

(2015) Ioanna Ntai et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow

(2015) Tanya Svinkina et al.   MOLECULAR & CELLULAR PROTEOMICS

Ion Coalescence of Neutron Encoded TMT 10-Plex Reporter Ions

(2014) Thilo Werner et al.   ANALYTICAL CHEMISTRY

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

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

Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

(2014) Tanveer S. Batth et al.   JOURNAL OF PROTEOME RESEARCH

Ischemia in Tumors Induces Early and Sustained Phosphorylation Changes in Stress Kinase Pathways but Does Not Affect Global Protein Levels

(2014) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification

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

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

Characterization of Breast Cancer Interstitial Fluids by TmT Labeling, LTQ-Orbitrap Velos Mass Spectrometry, and Pathway Analysis

(2012) Cinzia Raso et al.   JOURNAL OF PROTEOME RESEARCH

Model Studies on iTRAQ Modification of Peptides: Sequence-dependent Reaction Specificity

(2012) John E. Wiktorowicz et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics

(2011) Philipp Mertins et al.   MOLECULAR & CELLULAR PROTEOMICS

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

(2011) Craig D Wenger et al.   NATURE METHODS

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

(2011) Lily Ting et al.   NATURE METHODS

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Peptide Labeling with Isobaric Tags Yields Higher Identification Rates Using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap

(2010) Peter Pichler et al.   ANALYTICAL CHEMISTRY

Undesirable Charge-Enhancement of Isobaric Tagged Phosphopeptides Leads to Reduced Identification Efficiency

(2010) Tine E. Thingholm et al.   JOURNAL OF PROTEOME RESEARCH

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

(2010) Natasha A. Karp et al.   MOLECULAR & CELLULAR PROTEOMICS

Super-SILAC mix for quantitative proteomics of human tumor tissue

(2010) Tamar Geiger et al.   NATURE METHODS

Reversed-Phase-Reversed-Phase Liquid Chromatography Approach with High Orthogonality for Multidimensional Separation of Phosphopeptides

(2009) Chunxia Song et al.   ANALYTICAL CHEMISTRY

Practical Implementation of 2D HPLC Scheme with Accurate Peptide Retention Prediction in Both Dimensions for High-Throughput Bottom-Up Proteomics

(2008) Ravi C. Dwivedi et al.   ANALYTICAL CHEMISTRY

Temporal Profiling of the Adipocyte Proteome during Differentiation Using a Five-Plex SILAC Based Strategy

(2008) Henrik Molina et al.   JOURNAL OF PROTEOME RESEARCH

Does Trypsin Cut Before Proline?

(2007) Jesse Rodriguez et al.   JOURNAL OF PROTEOME RESEARCH