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EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data

Chalini D. Wijetunge, Isaam Saeed, Berin A. Boughton, Jeffrey M. Spraggins, Richard M. Caprioli, Antony Bacic, Ute Roessner, Saman K. Halgamuge
2015 Bioinformatics  
Methods: The proposed unsupervised algorithm uses Sliding Window Normalization (SWN) and a new spatial distribution based peak picking method developed based on Gray level Co-Occurrence (GCO) matrices  ...  Various data processing methods have been developed for exploring the resultant high volume data.  ...  Acknowledgements The authors thank the University of Melbourne-Vanderbilt University Partnership Grant Scheme and also the School of Botany node of Metabolomics Australia (MA) at The University of Melbourne, a  ... 
doi:10.1093/bioinformatics/btv356 pmid:26063840 fatcat:75lyjpho65godhmuf7kfznp7ri

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay, Artem Tarasov, Vitaly Kovalev, Jens Fuchser, Sergey Nikolenko, Charles Pineau, Michael Becker, Theodore Alexandrov
2016 Nature Methods  
This puts high demands on mass-based separation. The introduction of high-  ...  We developed the first bioinformatics framework for False Discovery Rate (FDR)-controlled metabolite annotation for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM  ...  We thank EMBL Core Facilities for instrumentation for LC-MS/MS analysis. TA thanks Pieter  ... 
doi:10.1038/nmeth.4072 pmid:27842059 fatcat:e2nheuwpqnaahjtouct5l7ltii

Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights

Amanda Rae Buchberger, Kellen DeLaney, Jillian Johnson, Lingjun Li
2017 Analytical Chemistry  
Overall, the aim of this review is to provide an informative resource for those in the MSI community who are interested in improving MSI data quality and analysis or using MSI for novel applications.  ...  mass spectrometry (MS) and visualization of spatial distributions in thin sample sections makes this a valuable chemical analysis tool for biological specimen characterization.  ...  There are a few different methods for normalization for MSI data sets based on the purpose of the analysis.  ... 
doi:10.1021/acs.analchem.7b04733 pmid:29155564 pmcid:PMC5959842 fatcat:dmkh3snt2bdofofmees5fxnfku

A year (2014-2015) of plants inProteomicsjournal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

Rosa Sanchez-Lucas, Angela Mehta, Luis Valledor, Francisco Cabello-Hurtado, M. Cristina Romero-Rodrıguez, Lyudmila Simova-Stoilova, Sekvan Demir, Luis E. Rodriguez-de-Francisco, Ana M. Maldonado-Alconada, Ana L. Jorrin-Prieto, Jesus V. Jorrín-Novo
2016 Proteomics  
30 The present review is an update of the previous one published in Proteomics 2015 Reviews special 31 issue [1] covering the 2014-July 2015 period.  ...  It has been written on the bases of the publications that 32 appeared in Proteomics journal during that period and the most relevant ones that have been published 33 in other high-impact journals.  ...  Acknowledgements 411 Thanks to the University of Córdoba (Programas Propio y de Fortalecimiento) and CNPq (AM, and 412 JVJN) for financial support.  ... 
doi:10.1002/pmic.201500351 pmid:26621614 fatcat:maar5nx27zfqtmwodtem3aj4qi