A collection of open source applications for mass spectrometry data mining

PROTEOMICS ◽  
2014 ◽  
Vol 14 (20) ◽  
pp. 2275-2279 ◽  
Author(s):  
Óscar Gallardo ◽  
David Ovelleiro ◽  
Marina Gay ◽  
Montserrat Carrascal ◽  
Joaquin Abian
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Open Source ◽  
Mass Spectrometry Data

Advancements in capturing and mining mass spectrometry data are transforming natural products research

2021 ◽  
Author(s):  
Scott A. Jarmusch ◽  
Justin J. J. van der Hooft ◽  
Pieter C. Dorrestein ◽  
Alan K. Jarmusch
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Natural Products ◽  
Data Analysis ◽  
Community Participation ◽  
Mass Spectrometry Data ◽  
Metabolomics Data ◽  
Analysis Tools ◽  
Public Data ◽  
Potential Use

This review covers the current and potential use of mass spectrometry-based metabolomics data mining in natural products. Public data, metadata, databases and data analysis tools are critical. The value and success of data mining rely on community participation.

scholarly journals MzJava: An open source library for mass spectrometry data processing

2015 ◽  
Vol 129 ◽  
pp. 63-70 ◽  
Author(s):  
Oliver Horlacher ◽  
Frederic Nikitin ◽  
Davide Alocci ◽  
Julien Mariethoz ◽  
Markus Müller ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Processing ◽  
Open Source ◽  
Mass Spectrometry Data

scholarly journals glyXtoolMS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data

2018 ◽  
Vol 90 (20) ◽  
pp. 11908-11916 ◽  
Author(s):  
Markus Pioch ◽  
Marcus Hoffmann ◽  
Alexander Pralow ◽  
Udo Reichl ◽  
Erdmann Rapp
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Mass Spectrometry Data

TOPPView: An Open-Source Viewer for Mass Spectrometry Data

2009 ◽  
Vol 8 (7) ◽  
pp. 3760-3763 ◽  
Author(s):  
Marc Sturm ◽  
Oliver Kohlbacher
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Mass Spectrometry Data

scholarly journals Bioinformatic Analysis of the Wound Peptidome Reveals Potential Biomarkers and Antimicrobial Peptides

2021 ◽  
Vol 11 ◽  
Author(s):  
Erik Hartman ◽  
Karl Wallblom ◽  
Mariena J. A. van der Plas ◽  
Jitka Petrlova ◽  
Jun Cai ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Open Source ◽  
Medical Condition ◽  
Unmet Need ◽  
Mass Spectrometry Data ◽  
Wound Dressings ◽  
Diagnostic Tools ◽  
Wound Fluid ◽  
Sorting Algorithms ◽  
Infected Wounds

Wound infection is a common and serious medical condition with an unmet need for improved diagnostic tools. A peptidomic approach, aided by mass spectrometry and bioinformatics, could provide novel means of identifying new peptide biomarkers for wound healing and infection assessment. Wound fluid is suitable for peptidomic analysis since it is both intimately tied to the wound environment and is readily available. In this study we investigate the peptidomes of wound fluids derived from surgical drainages following mastectomy and from wound dressings following facial skin grafting. By applying sorting algorithms and open source third party software to peptidomic label free tandem mass spectrometry data we provide an unbiased general methodology for analyzing and differentiating between peptidomes. We show that the wound fluid peptidomes of patients are highly individualized. However, differences emerge when grouping the patients depending on wound type. Furthermore, the abundance of peptides originating from documented antimicrobial regions of hemoglobin in infected wounds may contribute to an antimicrobial wound environment, as determined by in silico analysis. We validate our findings by compiling literature on peptide biomarkers and peptides of physiological significance and cross checking the results against our dataset, demonstrating that well-documented peptides of immunological significance are abundant in infected wounds, and originate from certain distinct regions in proteins such as hemoglobin and fibrinogen. Ultimately, we have demonstrated the power using sorting algorithms and open source software to help yield insights and visualize peptidomic data.

scholarly journals OpenMS: a flexible open-source software platform for mass spectrometry data analysis

2016 ◽  
Vol 13 (9) ◽  
pp. 741-748 ◽  
Author(s):  
Hannes L Röst ◽  
Timo Sachsenberg ◽  
Stephan Aiche ◽  
Chris Bielow ◽  
Hendrik Weisser ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Mass Spectrometry Data ◽  
Software Platform

scholarly journals Fast Elastic Peak Detection for Mass Spectrometry Data Mining

2012 ◽  
Vol 24 (4) ◽  
pp. 634-648 ◽  
Author(s):  
Xin Zhang ◽  
Dennis E. Shasha ◽  
Yang Song ◽  
Jason T. L. Wang
Keyword(s):  
Mass Spectrometry ◽  
Data Mining ◽  
Peak Detection ◽  
Mass Spectrometry Data ◽  
Elastic Peak
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