Computational Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage and Applications to 15 Tumors

Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry

(2020) Kyung-Cho Cho et al.   ANALYTICAL CHEMISTRY

Accelerated Lysis and Proteolytic Digestion of Biopsy-Level Fresh-Frozen and FFPE Tissue Samples Using Pressure Cycling Technology

(2020) Huanhuan Gao et al.   JOURNAL OF PROTEOME RESEARCH

Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020

(2020) Fangfei Zhang et al.   PROTEOMICS

Generating Proteomic Big Data for Precision Medicine

(2020) Yue Liang et al.   PROTEOMICS

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

(2020) Tiansheng Zhu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins

(2019) Peter Blattmann et al.   Scientific Data

Systematic Assessment of the Effect of Internal Library in Targeted Analysis of SWATH-MS

(2019) Chuan-Qi Zhong et al.   JOURNAL OF PROTEOME RESEARCH

Reproducibility, specificity and accuracy of relative quantification using spectral library-based data-independent acquisition

(2019) Katalin Barkovits et al.   MOLECULAR & CELLULAR PROTEOMICS

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

Arabidopsis proteome and the mass spectral assay library

(2019) Huoming Zhang et al.   Scientific Data

Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics

(2017) Johan Teleman et al.   JOURNAL OF PROTEOME RESEARCH

Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

(2017) George Rosenberger et al.   NATURE METHODS

SWATH Mass Spectrometry Performance Using Extended Peptide MS/MS Assay Libraries

(2016) Jemma X. Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

Effect of peptide assay library size and composition in targeted data-independent acquisition-MS analyses

(2016) Sarah J. Parker et al.   PROTEOMICS

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

(2015) Tiannan Guo et al.   NATURE MEDICINE

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Building high-quality assay libraries for targeted analysis of SWATH MS data

(2015) Olga T Schubert et al.   Nature Protocols

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

(2014) Jin Zi et al.   ANALYTICAL CHEMISTRY

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

A repository of assays to quantify 10,000 human proteins by SWATH-MS

(2014) George Rosenberger et al.   Scientific Data

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

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

(2012) Claudia Escher et al.   PROTEOMICS