scholarly journals Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

2016 ◽  
Author(s):  
Hannes L Röst ◽  
Ruedi Aebersold ◽  
Olga T Schubert
Keyword(s):  
Data Analysis ◽  
High Accuracy ◽  
Error Rates ◽  
Selected Reaction Monitoring ◽  
Reaction Monitoring ◽  
Specific Mass ◽  
Quantitative Accuracy ◽  
Analysis Workflow ◽  
Control Of Error ◽  
Automated Data Analysis

Targeted mass spectrometry comprises a set of methods able to quantify protein analytes in complex mixtures with high accuracy and sensitivity. These methods, e.g., Selected Reaction Monitoring (SRM) and SWATH MS, use specific mass spectrometric coordinates (assays) for reproducible detection and quantification of proteins. In this protocol, we describe how to analyze in a targeted manner data from a SWATH MS experiment aimed at monitoring thousands of proteins reproducibly over many samples. We present a standard SWATH MS analysis workflow, including manual data analysis for quality control (based on Skyline) as well as automated data analysis with appropriate control of error rates (based on the OpenSWATH workflow). We also discuss considerations to ensure maximal coverage, reproducibility and quantitative accuracy.

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies

2013 ◽  
Vol 8 (8) ◽  
pp. 1602-1619 ◽  
Author(s):  
Silvia Surinova ◽  
Ruth Hüttenhain ◽  
Ching-Yun Chang ◽  
Lucia Espona ◽  
Olga Vitek ◽  
...  
Keyword(s):  
Data Analysis ◽  
Large Scale ◽  
Monitoring Data ◽  
Selected Reaction Monitoring ◽  
Reaction Monitoring ◽  
Analysis Workflow

scholarly journals Simultaneous control of error rates in fMRI data analysis

NeuroImage ◽  
2015 ◽  
Vol 123 ◽  
pp. 102-113 ◽  
Author(s):  
Hakmook Kang ◽  
Jeffrey Blume ◽  
Hernando Ombao ◽  
David Badre
Keyword(s):  
Data Analysis ◽  
Error Rates ◽  
Fmri Data ◽  
Simultaneous Control ◽  
Fmri Data Analysis ◽  
Control Of Error

Mass spectrometry-based proteomics in biomedical research: emerging technologies and future strategies

2010 ◽  
Vol 12 ◽  
Author(s):  
Geraldine M. Walsh ◽  
Jason C. Rogalski ◽  
Cordula Klockenbusch ◽  
Juergen Kast
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Biomedical Research ◽  
Biological Systems ◽  
Basic Research ◽  
Selected Reaction Monitoring ◽  
Reaction Monitoring ◽  
Peptide Separation ◽  
Standard Methods ◽  
Biochemical Fractionation

In recent years, the technology and methods widely available for mass spectrometry (MS)-based proteomics have increased in power and potential, allowing the study of protein-level processes occurring in biological systems. Although these methods remain an active area of research, established techniques are already helping answer biological questions. Here, this recent evolution of MS-based proteomics and its applications are reviewed, including standard methods for protein and peptide separation, biochemical fractionation, quantitation, targeted MS approaches such as selected reaction monitoring, data analysis and bioinformatics. Recent research in many of these areas reveals that proteomics has moved beyond simply cataloguing proteins in biological systems and is finally living up to its initial potential – as an essential tool to aid related disciplines, notably health research. From here, there is great potential for MS-based proteomics to move beyond basic research, into clinical research and diagnostics.

scholarly journals SRMBUILDER: A USER-FRIENDLY TOOL FOR SELECTED REACTION MONITORING DATA ANALYSIS

2011 ◽  
Vol 09 (supp01) ◽  
pp. 51-62 ◽  
Author(s):  
QUANHU SHENG ◽  
CHAOCHAO WU ◽  
ZHIDUAN SU ◽  
RONG ZENG
Keyword(s):  
Data Analysis ◽  
Software Tool ◽  
High Sensitivity ◽  
Selected Reaction Monitoring ◽  
Reaction Monitoring ◽  
Post Translational Modification ◽  
Research Areas ◽  
File Formats ◽  
Data Files ◽  
User Friendly

With high sensitivity and reproducibility, selected reaction monitoring (SRM) has become increasingly popular in proteome research for targeted quantification of low abundance proteins and post translational modification. SRM is also well accepted in other mass-spectrometry based research areas such as lipidomics and metabolomics, which necessitates the development of easy-to-use software for both post-acquisition SRM data analysis and quantification result validation. Here, we introduce a software tool SRMBuilder, which can automatically parse SRM data in multiple file formats, assign transitions to compounds, match light/heavy transition/compound pairs and provide a user-friendly graphic interface to manually validate the quantification result at transition/compound/sample level. SRMBuilder will greatly facilitate processing of the post-acquisition data files and validation of quantification result for SRM. The software can be downloaded for free from as part of the software suite ProteomicsTools.

Sign in / Sign up

Export Citation Format

Share Document