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Automated workflow composition in mass spectrometry based proteomics

Magnus Palmblad, Anna-Lena Lamprecht, Jon Ison, Veit Schwämmle, Jonathan Wren
2018 Bioinformatics  
Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows.  ...  Working out which tools and combinations are applicable or optimal in practice is often hard.  ...  We explore the value of formalized semantic tool descriptions for guided construction of practical workflows for mass spectrometry (MS)-based proteomics.  ... 
doi:10.1093/bioinformatics/bty646 pmid:30060113 pmcid:PMC6378944 fatcat:ev5w2fvdkvaxzofrfusrmnklx4

D1.8 Tools Interoperability And Service Registry

Magnus Palmblad, Anna-Lena Lamprecht, Veit Schwämmle, Jon Ison
2018 Zenodo  
Automated workflow composition in mass spectrometry based proteomics Accepted for publication in Bioinformatics The first article (Tsiamis et†al†.) describes a systematic approach towards the comprehensive  ...  Community curation of software tools as illustrated for mass spectrometry based proteomics In preparation¨see https://tinyurl.com/proteomics-tools Palmblad, M., Lamprecht, A., Ison, J. and Schwämmle, V  ...  Automated workflow composition in mass spectrometry based proteomics. Accepted for publication in Bioinformatics. See Section 3.2.  ... 
doi:10.5281/zenodo.1456766 fatcat:hply4krokvfsroveizv3c7pdwi

What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics

Hamid Hamzeiy, Jürgen Cox
2017 Current Opinion in Biotechnology  
Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps.  ...  We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics.  ...  Introduction Mass spectrometry-based proteomics [1, 2, 3 ] has matured during recent years to a degree that makes it readily usable as a standard research tool in many branches of biological and biomedical  ... 
doi:10.1016/j.copbio.2016.11.014 pmid:28039739 fatcat:ok3ld24hvvb47necwynne66ky4

Report of the 23rd Asilomar Conference on Mass Spectrometry

A ROCKWOOD, R SINGH
2008 Journal of the American Society for Mass Spectrometry  
He discussed a number of automation tools employed at LabCorp in development and application of LC-MS/MS workflows, including smart automation tools in optimization of method development.  ...  The session concluded with "Automated Nucleic Acid Based Signature Sequence Analysis by MALDI-TOF Mass Spectrometry-a Comparative Sequence Analysis Tool" by Christiane Honisch, Ph.D., SEQUENOM, Inc.  ... 
doi:10.1016/j.jasms.2008.04.022 pmid:18485729 fatcat:fpapuecjrba7leeeil72tdje4u

Implementation and Application of Data-Independent Acquisition Workflows in a Mass Spectrometry Facility

Birgit Schilling
2019 Journal of Biomolecular Techniques  
Proteomics workflows in mass spectrometric core facilities require great flexibility and adaptation to the individual projects, providing high quality data sets for diverse sets of projects.  ...  We demonstrate the use of data-independent acquisition DIA workflows in our proteomics core for a wide variety of collaborative projects, representing at times small studies or larger scale projects.  ...  Vanderbilt University Hydrogen-deuterium exchange (HDX) mass spectrometry and imaging mass spectrometry (IMS) are two cutting edge mass spectrometry techniques that are not frequently found in Core facilities  ... 
pmid:31897001 pmcid:PMC6938116 fatcat:uq62vzhejvgrrlxbnbr42y5m7m

Protein-species quantitative venomics: looking through a crystal ball

Juan J. Calvete, Daniel Petras, Francisco Calderón-Celis, Bruno Lomonte, Jorge Ruiz Encinar, Alfredo Sanz-Medel
2017 Journal of Venomous Animals and Toxins including Tropical Diseases  
In this paper we discuss recent significant developments in the field of venom research, specifically the emergence of top-down proteomic applications that allow achieving compositional resolution at the  ...  Challenges remain to be solved in order to achieve a compact and automated platform with which to routinely carry out comprehensive quantitative analysis of all toxins present in a venom.  ...  In addition, they all read and approved the final manuscript.  ... 
doi:10.1186/s40409-017-0116-9 pmid:28465678 pmcid:PMC5408492 fatcat:ctvzwkbjercebhae2whrka6bwu

Computational Mass Spectrometry–Based Proteomics

Lukas Käll, Olga Vitek, Fran Lewitter
2011 PLoS Computational Biology  
The overall mass spectrometry-based proteomic workflow is summarized in Figure 1 .  ...  Figure 1 .Figure 2 . 12 Quantitative mass spectrometry-based proteomic workflow.  ... 
doi:10.1371/journal.pcbi.1002277 pmid:22144880 pmcid:PMC3228769 fatcat:gpro6czogjcudlp6gvggxtnfx4

An automated workflow for the discovery and docking simulation of the protein-protein complexes using in vivo chemical cross-linking [article]

Vladimir Svetlov, Evgeny Nudler
2018 bioRxiv   pre-print
We report an automated/score driven workflow of discovery and structural interrogation of protein-protein complexes in vivo by means of chemical cross-linking.  ...  This streamlined workflow is illustrated by the discovery of the direct interactions in vivo between E. coli RNAP polymerase and the transcription elongation factor NusA, using chemical cross-linking as  ...  Given the focus of this work on the automated, score-driven workflow we have selected cluster 1 as the docking outcome based on its superior scores, as provided by HADDOCK.  ... 
doi:10.1101/373829 fatcat:iytn5ansszgntcnqld64vccun4

Single Cell Proteome Mapping of Tissue Heterogeneity Using Microfluidic Nanodroplet Sample Processing and Ultrasensitive LC-MS

Ryan Kelly, Ying Zhu, Yiran Liang, Yongzheng Cong, Paul Piehowski, Maowei Dou, Rui Zhao, Wei-Jun Qian, Kristin Burnum-Johnson, Charles Ansong
2019 Journal of Biomolecular Techniques  
Single cells can be isolated into nanowells by fluorescence-activated cell sorting (FACS) or laser capture dissection (LCM), processed, and analyzed with low-flow nanoLC Orbitrap mass spectrometry.  ...  While MS-based proteomic analyses are capable of quantifying thousands of proteins, the extension to single cell studies has been largely ineffective.  ...  1 Brigham Young University and Pacific Northwest National Laboratory, 2 Pacific Northwest National Laboratory, 3 Brigham Young University, 4 Imaging and Spatially Explicit Mass Spectrometry Biological  ... 
pmid:31897031 pmcid:PMC6938103 fatcat:vpcgmcu5kvepvklpbu6w4ymxku

Bottom-Up Mass Spectrometry–Based Proteomics as an Investigative Analytical Tool for Discovery and Quantification of Proteins in Biological Samples

Ravi Amunugama, Richard Jones, Michael Ford, David Allen
2013 Advances in Wound Care  
Objective: The objective of this overview is to introduce bottom-up mass spectrometry (MS)-based proteomics approaches and strategies, widely used in other biomedical research fields, to the wound-healing  ...  chromatographytandem mass spectrometry analysis.  ...  INNOVATION Recent advances in MS platforms A typical bottom-up MS-based proteomics workflow is illustrated in Figure 2 .  ... 
doi:10.1089/wound.2012.0384 pmid:24761338 pmcid:PMC3842888 fatcat:y65atkbifjhc5j57vpuvzk4nhm

Integration of Bioinformatics Tools for Proteomics Research

Tushar Nanda, Kadambini Tripathy
2011 Journal of computer science and systems biology  
Emerging proteomic technologies have promised for early diagnosis and in advancing treatment directions.  ...  This review presents a general survey of the recent development in array technologies from a proteomics perspective.  ...  A novel mass spectrometry (MS)-based approach to the identification of host-derived biomarkers (BMs) in the circulating low-molecularmass serum proteome was tested [54] .  ... 
doi:10.4172/jcsb.s13-002 fatcat:k3d5kuw3vbcxzi5a3dopmmnlwq

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

Toan K Phung, Cassandra L Pegg, Benjamin L Schulz
2020 Beilstein Journal of Organic Chemistry  
Mass spectrometry glycoproteomics is rapidly maturing, allowing unprecedented insights into the diversity and functions of protein glycosylation.  ...  We developed GlypNirO, an automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis  ...  With that comes the need for robust and automated workflows for extracting meaningful results.  ... 
doi:10.3762/bjoc.16.180 pmid:32952729 pmcid:PMC7476601 fatcat:27iiqyhjujcjxi36bn2qdglyja

Solid-Phase Extraction Strategies to Surmount Body Fluid Sample Complexity in High-Throughput Mass Spectrometry-Based Proteomics

Marco R. Bladergroen, Yuri E. M. van der Burgt
2015 Journal of Analytical Methods in Chemistry  
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential.  ...  The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches.  ...  Introduction Sample preparation of biological specimens is an essential part in any mass spectrometry-(MS-) based proteomics experiment since body fluids as well as tissue sections are highly complex in  ... 
doi:10.1155/2015/250131 pmid:25692071 pmcid:PMC4322654 fatcat:da3u5ijfdbbl7dv4wdnpnoqm5e

Chromatin proteomics to study epigenetics – challenges and opportunities

Guido van Mierlo, Michiel Vermeulen
2020 Molecular & Cellular Proteomics  
Mass spectrometry-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in  ...  Total chromatin isolated from cells can be directly analysed using mass spectrometry or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis.  ...  For ChIP-based methods automated workflows are available (78, 79) but it is not clear whether these will allow purifying sufficient protein amounts for mass spectrometry-based studies.  ... 
doi:10.1074/mcp.r120.002208 pmid:33060119 pmcid:PMC7973309 fatcat:qi4xlgxsv5dodafhr5mnviipre

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

Hannes L Röst, Timo Sachsenberg, Stephan Aiche, Chris Bielow, Hendrik Weisser, Fabian Aicheler, Sandro Andreotti, Hans-Christian Ehrlich, Petra Gutenbrunner, Erhan Kenar, Xiao Liang, Sven Nahnsen (+15 others)
2016 Nature Methods  
We are deeply grateful for the support of the KNIME team, the Proteome Discoverer team, and the Compound Discoverer team.  ...  The OpenMS project is one of multiple software solutions addressing the computational challenges of mass spectrometry-based proteomics, each contributing in different areas such as protein inference, peptide  ...  Editorial summary: OpenMS is a flexible, user-friendly, open-source software platform for the biological analysis of mass spectrometry proteomics and metabolomics data.  ... 
doi:10.1038/nmeth.3959 pmid:27575624 fatcat:khqavbue6zepvpbsfzmkwcg6ly
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