Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non-small cell lung cancer

Use of Fast HPLC Multiple Reaction Monitoring Cubed for Endogenous Retinoic Acid Quantification in Complex Matrices

(2015) Jace W. Jones et al.   ANALYTICAL CHEMISTRY

mTOR in health and in sickness

(2015) Dritan Liko et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence

(2015) Erik L. de Graaf et al.   JOURNAL OF PROTEOME RESEARCH

Quantitation of 47 human tear proteins using high resolution multiple reaction monitoring (HR-MRM) based-mass spectrometry

(2015) Louis Tong et al.   Journal of Proteomics

Detection and quantification of proteins in clinical samples using high resolution mass spectrometry

(2015) Sebastien Gallien et al.   METHODS

Molecular Architecture of 4E-BP Translational Inhibitors Bound to eIF4E

(2015) Daniel Peter et al.   MOLECULAR CELL

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry

(2015) Shiying Shao et al.   PROTEOMICS

Using data-independent, high-resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications

(2015) Tatjana Sajic et al.   Proteomics Clinical Applications

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Current treatment strategies for inhibiting mTOR in cancer

(2015) Francesca Chiarini et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas

(2015) Piero Giansanti et al.   Cell Reports

Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry

(2015) Benjamin L. Parker et al.   Science Signaling

Expansion of the Ion Library for Mining SWATH-MS Data through Fractionation Proteomics

(2014) Jin Zi et al.   ANALYTICAL CHEMISTRY

Variation and quantification among a target set of phosphopeptides in human plasma by multiple reaction monitoring and SWATH-MS2 data-independent acquisition

(2014) Anna M. Zawadzka et al.   ELECTROPHORESIS

Evaluation of Data-Dependent and -Independent Mass Spectrometric Workflows for Sensitive Quantification of Proteins and Phosphorylation Sites

(2014) Manuel Bauer 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

Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution

(2014) Erik L. de Graaf et al.   MOLECULAR & CELLULAR PROTEOMICS

ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma

(2014) M. A. Smit et al.   Molecular Systems Biology

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

A sentinel protein assay for simultaneously quantifying cellular processes

(2014) Martin Soste et al.   NATURE METHODS

Overcoming biofluid protein complexity during targeted mass spectrometry detection and quantification of protein biomarkers by MRM cubed (MRM3)

(2013) Jeremy Jeudy et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Optimization of liquid chromatography–multiple reaction monitoring cubed mass spectrometry assay for protein quantification: Application to aquaporin-2 water channel in human urine

(2013) Aurore Jaffuel et al.   JOURNAL OF CHROMATOGRAPHY A

MS3 fragmentation patterns of monomethylarginine species and the quantification of all methylarginine species in yeast using MRM3

(2013) Ted M. Lakowski et al.   Journal of Proteomics

Technical considerations for large-scale parallel reaction monitoring analysis

(2013) Sebastien Gallien et al.   Journal of Proteomics

Robust phosphoproteome enrichment using monodisperse microsphere–based immobilized titanium (IV) ion affinity chromatography

(2013) Houjiang Zhou et al.   Nature Protocols

Targeting mTOR to Overcome Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Resistance in Non-Small Cell Lung Cancer Cells

(2013) Shi-Jiang Fei et al.   PLoS One

In-house construction of a UHPLC system enabling the identification of over 4000 protein groups in a single analysis

(2012) Alba Cristobal et al.   ANALYST

The current status of clinical proteomics and the use of MRM and MRM3for biomarker validation

(2012) Jérôme Lemoine et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Next-generation proteomics: towards an integrative view of proteome dynamics

(2012) A. F. Maarten Altelaar et al.   NATURE REVIEWS GENETICS

Phosphorylation of Raptor by p38β Participates in Arsenite-induced Mammalian Target of Rapamycin Complex 1 (mTORC1) Activation

(2011) Xiao-Nan Wu et al.   JOURNAL OF BIOLOGICAL 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

Protein Significance Analysis in Selected Reaction Monitoring (SRM) Measurements

(2011) Ching-Yun Chang et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2011) Lukas Reiter et al.   NATURE METHODS

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

(2010) Brendan MacLean et al.   BIOINFORMATICS

Mammalian Ste20-like Kinase (Mst2) Indirectly Supports Raf-1/ERK Pathway Activity via Maintenance of Protein Phosphatase-2A Catalytic Subunit Levels and Consequent Suppression of Inhibitory Raf-1 Phosphorylation

(2010) Geoffrey K. Kilili et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Measurement of Protein Phosphorylation Stoichiometry by Selected Reaction Monitoring Mass Spectrometry

(2010) Lily L. Jin et al.   JOURNAL OF PROTEOME RESEARCH

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum

(2009) T. Fortin et al.   ANALYTICAL CHEMISTRY

The phosphoproteomics data explosion

(2009) Simone Lemeer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Site-Specific mTOR Phosphorylation Promotes mTORC1-Mediated Signaling and Cell Growth

(2009) H. A. Acosta-Jaquez et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2009) Paola Picotti et al.   NATURE METHODS

Analytical strategies for phosphoproteomics

(2009) Tine E. Thingholm et al.   PROTEOMICS

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

(2008) Boris Macek et al.   Annual Review of Pharmacology and Toxicology

Quantitative phosphoproteomic analysis of signaling network dynamics

(2008) Forest M White   CURRENT OPINION IN BIOTECHNOLOGY

Negative and Positive Regulation of MAPK Phosphatase 3 Controls Platelet-derived Growth Factor-induced Erk Activation

(2008) Aleksandra Jurek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Proline-rich Akt Substrate of 40 kDa (PRAS40) Function by Mammalian Target of Rapamycin Complex 1 (mTORC1)-mediated Phosphorylation

(2008) Lifu Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY