Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

(2014) George Rosenberger et al.   BIOINFORMATICS

iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations

(2014) Peter Kunszt et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Renal Tumors

(2013) Puay Hoon Tan et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system

(2013) Ben C Collins et al.   NATURE METHODS

Quantitative measurements ofN-linked glycoproteins in human plasma by SWATH-MS

(2013) Yansheng Liu et al.   PROTEOMICS

Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion

(2012) Timo Glatter et al.   JOURNAL OF PROTEOME RESEARCH

Expanding the Chemical Cross-Linking Toolbox by the Use of Multiple Proteases and Enrichment by Size Exclusion Chromatography

(2012) Alexander Leitner 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

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Using iRT, a normalized retention time for more targeted measurement of peptides

(2012) Claudia Escher et al.   PROTEOMICS

Current Pathology Keys of Renal Cell Carcinoma

(2011) Ferran Algaba et al.   EUROPEAN UROLOGY

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Options and considerations when selecting a quantitative proteomics strategy

(2010) Bruno Domon et al.   NATURE BIOTECHNOLOGY

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

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

(2009) Paola Picotti et al.   CELL

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression

(2009) Arun Sreekumar et al.   NATURE

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

Gene-Expression Signatures in Breast Cancer

(2009) Christos Sotiriou et al.   NEW ENGLAND JOURNAL OF MEDICINE

ProteoWizard: open source software for rapid proteomics tools development

(2008) Darren Kessner et al.   BIOINFORMATICS

OpenMS – An open-source software framework for mass spectrometry

(2008) Marc Sturm et al.   BMC BIOINFORMATICS

Application of Pressurized Solvents for Ultrafast Trypsin Hydrolysis in Proteomics: Proteomics on the Fly

(2008) Daniel López-Ferrer et al.   JOURNAL OF PROTEOME RESEARCH

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH