scholarly journals xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data

2019 ◽  
Author(s):  
Martin Graham ◽  
Colin Combe ◽  
Lars Kolbowski ◽  
Juri Rappsilber
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Data Standards ◽  
Downstream Analysis ◽  
Common Platform

AbstractxiView provides a common platform for the downstream analysis and visualisation of Crosslinking Mass Spectrometry data. It is independent of the search software used and its input is compliant with the relevant mass spectrometry data standards. It uses established visualisation techniques, notably Multiple Coordinated Views, to help the user explore the data and is designed to facilitate comparisons between different datasets.

scholarly journals Normalization of Mass Spectrometry Data (NOMAD)

2017 ◽  
Author(s):  
Carl Murie ◽  
Brian Sandri ◽  
Timothy J. Griffin ◽  
Christine Wendt ◽  
Ola Larsson
Keyword(s):  
Mass Spectrometry ◽  
Reference Sample ◽  
R Package ◽  
Mass Spectrometry Data ◽  
Bioconductor Package ◽  
Computationally Efficient ◽  
Itraq Reagent ◽  
Downstream Analysis ◽  
Larger Sample ◽  
Model Approach

AbstractMotivationiTRAQ reagent-based mass spectrometry (MS) is a commonly used technology for identification and quantification of proteins in biological samples. Such studies are often performed over multiple MS runs, potentially resulting in introduction of MS run bias that could affect downstream analysis. iTRAQ MS data have therefore commonly been normalized using a reference sample which is included in each MS run. We show, however, that such normalization does not efficiently remove systematic MS run bias. A linear model approach was previously proposed to improve on the reference normalization approach but does not computationally scale to larger data. Here we describe the NOMAD (normalization of mass spectrometry data) R package which implements a computationally efficient ANOVA normalization approach with protein assembly functionality.ResultsNOMAD provides the same advantages as the linear regression solution but is more computationally efficient which allows superior scaling to larger sample sizes. Moreover, NOMAD efficiently removes bias which allows for valid across MS run comparisons.AvailabilityThe NOMAD Bioconductor package: [email protected]; [email protected]

154: Integration of TPSA and High-Throughput Mass Spectrometry Data Improves Prostate Cancer Prediction

2007 ◽  
Vol 177 (4S) ◽  
pp. 52-53
Author(s):  
Stefano Ongarello ◽  
Eberhard Steiner ◽  
Regina Achleitner ◽  
Isabel Feuerstein ◽  
Birgit Stenzel ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Cancer Prediction

Nonparametric Pre-Processing Methods and Inference Tools for Analyzing Time-of-Flight Mass Spectrometry Data.

2007 ◽  
Vol 3 (2) ◽  
pp. 127-147 ◽  
Author(s):  
Anestis Antoniadis ◽  
Jeremie Bigot ◽  
Sophie Lambert-Lacroix ◽  
Frederique Letue
Keyword(s):  
Mass Spectrometry ◽  
Time Of Flight ◽  
Mass Spectrometry Data ◽  
Processing Methods ◽  
Flight Mass Spectrometry

Interlaboratory Comparison of Untargeted Mass Spectrometry Data Uncovers Underlying Causes for Variability

2021 ◽  
Author(s):  
Trevor N. Clark ◽  
Joëlle Houriet ◽  
Warren S. Vidar ◽  
Joshua J. Kellogg ◽  
Daniel A. Todd ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Interlaboratory Comparison ◽  
Mass Spectrometry Data ◽  
Underlying Causes

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 mzML—a Community Standard for Mass Spectrometry Data

2010 ◽  
Vol 10 (1) ◽  
pp. R110.000133 ◽  
Author(s):  
Lennart Martens ◽  
Matthew Chambers ◽  
Marc Sturm ◽  
Darren Kessner ◽  
Fredrik Levander ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Community Standard
Sign in / Sign up

Export Citation Format

Share Document