OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data

Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry

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

Trapped ion mobility spectrometry and PASEF enable in-depth lipidomics from minimal sample amounts

(2020) Catherine G. Vasilopoulou et al.   Nature Communications

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

(2020) Dorte B. Bekker-Jensen et al.   Nature Communications

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

(2020) Nikita Prianichnikov et al.   MOLECULAR & CELLULAR PROTEOMICS

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

(2020) Fengchao Yu et al.   MOLECULAR & CELLULAR PROTEOMICS

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

(2020) Babara Steigenberger et al.   MOLECULAR & CELLULAR PROTEOMICS

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

(2020) Florian Meier et al.   NATURE METHODS

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

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

(2019) Vadim Demichev et al.   NATURE METHODS

Generation of a Collision Cross Section Library for Multi-Dimensional Plant Metabolomics Using UHPLC-Trapped Ion Mobility-MS/MS

(2019) Mark Schroeder et al.   Metabolites

Hybrid ion mobility and mass spectrometry as a separation tool

(2016) Michael A. Ewing et al.   JOURNAL OF CHROMATOGRAPHY A

Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics

(2016) Ute Distler et al.   Nature Protocols

Parallel Accumulation–Serial Fragmentation (PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized Scans in a Trapped Ion Mobility Device

(2015) Florian Meier et al.   JOURNAL OF PROTEOME RESEARCH

Rcpp: SeamlessRandC++Integration

(2015) Dirk Eddelbuettel et al.   Journal of Statistical Software

Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

(2014) Dominic Helm et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2014) Hannes L Röst et al.   NATURE BIOTECHNOLOGY

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

(2013) Ute Distler et al.   NATURE METHODS

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 NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Radiation Metabolomics. 3. Biomarker Discovery in the Urine of Gamma-Irradiated Rats Using a Simplified Metabolomics Protocol of Gas Chromatography-Mass Spectrometry Combined with Random Forests Machine Learning Algorithm

(2009) Christian Lanz et al.   RADIATION RESEARCH