MSPolyCalc: A web‐based App for polymer mass spectrometry data interpretation. The case study of a pharmaceutical excipient

2020 ◽  
Vol 34 (S2) ◽  
Author(s):  
Jessica S. Desport ◽  
Gilles Frache ◽  
Luc Patiny
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Mass Spectrometry Data ◽  
Web Based ◽  
Pharmaceutical Excipient

Aom 2 S: A new web‐based application for DNA/RNA tandem mass spectrometry data interpretation

2020 ◽  
Vol 34 (23) ◽  
Author(s):  
Daniel Ortiz ◽  
Natalia Gasilova ◽  
Francisco Sepulveda ◽  
Luc Patiny ◽  
Paul J. Dyson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Data Interpretation ◽  
Mass Spectrometry Data ◽  
Tandem Mass ◽  
Web Based ◽  
Tandem Mass Spectrometry Data

TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation

2020 ◽  
Author(s):  
In Kwon Choi ◽  
Eroma Abeysinghe ◽  
Eric Coulter ◽  
Suresh Marru ◽  
Marlon Pierce ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Mass Spectrometry Data ◽  
Top Down ◽  
Top Down Mass Spectrometry

scholarly journals Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

2016 ◽  
Vol 15 (11) ◽  
pp. 3961-3970 ◽  
Author(s):  
Eric W. Deutsch ◽  
Christopher M. Overall ◽  
Jennifer E. Van Eyk ◽  
Mark S. Baker ◽  
Young-Ki Paik ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Human Proteome ◽  
Mass Spectrometry Data ◽  
Human Proteome Project

scholarly journals A synthetic peptide library for benchmarking crosslinking mass spectrometry search engines

2019 ◽  
Author(s):  
Rebecca Beveridge ◽  
Johannes Stadlmann ◽  
Josef M. Penninger ◽  
Karl Mechtler
Keyword(s):  
Mass Spectrometry ◽  
False Discovery Rate ◽  
Search Engines ◽  
Synthetic Peptide ◽  
External Validation ◽  
Data Interpretation ◽  
Peptide Libraries ◽  
Mass Spectrometry Data ◽  
Biological Interactions ◽  
False Discovery

We have created synthetic peptide libraries to benchmark crosslinking mass spectrometry search engines for different types of crosslinker. The unique benefit of using a library is knowing which identified crosslinks are true and which are false. Here we have used mass spectrometry data generated from measurement of the peptide libraries to evaluate the most frequently applied search algorithms in crosslinking mass-spectrometry. When filtered to an estimated false discovery rate of 5%, false crosslink identification ranged from 5.2% to 11.3% for search engines with inbuilt validation strategies for error estimation. When different external validation strategies were applied to one single search output, false crosslink identification ranged from 2.4% to a surprising 32%, despite being filtered to an estimated 5% false discovery rate. Remarkably, the use of MS-cleavable crosslinkers did not reduce the false discovery rate compared to non-cleavable crosslinkers, results from which have far-reaching implications in structural biology. We anticipate that the datasets acquired during this research will further drive optimisation and development of search engines and novel data-interpretation technologies, thereby advancing our understanding of vital biological interactions.

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