TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation.
Apache Airavata
Applied computing → Bioinformatics
Information systems → Computing platforms
Proteomics
SciGaP
Science Gateways
Top-down mass spectrometry
XSEDE
Journal
PEARC20 : Practice and Experience in Advanced Research Computing 2020 : Catch the wave : July 27-31, 2020, Portland, Or Virtual Conference. Practice and Experience in Advanced Research Computing (Conference) (2020 : Online)
Titre abrégé: PEARC20 (2020)
Pays: United States
ID NLM: 9918317681706676
Informations de publication
Date de publication:
Jul 2020
Jul 2020
Historique:
entrez:
26
5
2022
pubmed:
1
7
2020
medline:
1
7
2020
Statut:
ppublish
Résumé
Top-down mass spectrometry-based proteomics has become the method of choice for identifying and quantifying intact proteoforms in biological samples. We present a web-based gateway for TopPIC suite, a widely used software suite consisting of four software tools for top-down mass spectrometry data interpretation: TopFD, TopPIC, TopMG, and TopDiff. The gateway enables the community to use heterogeneous collection of computing resources that includes high performance computing clusters at Indiana University and virtual clusters on XSEDE's Jetstream Cloud resource for top-down mass spectral data analysis using TopPIC suite. The gateway will be a useful resource for proteomics researchers and students who have limited access to high-performance computing resources or who are not familiar with interacting with server-side supercomputers.
Identifiants
pubmed: 35615582
doi: 10.1145/3311790.3400853
pmc: PMC9128478
mid: NIHMS1622494
doi:
Types de publication
Journal Article
Langues
eng
Pagination
461-464Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM118470
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG065181
Pays : United States
Références
Nature. 2003 Mar 13;422(6928):198-207
pubmed: 12634793
J Am Soc Mass Spectrom. 2010 Feb;21(2):193-202
pubmed: 19942451
Bioinformatics. 2016 Nov 15;32(22):3495-3497
pubmed: 27423895
J Proteome Res. 2019 Mar 1;18(3):878-889
pubmed: 30638379
Bioinformatics. 2017 May 1;33(9):1309-1316
pubmed: 28453668
Mol Cell Proteomics. 2010 Dec;9(12):2772-82
pubmed: 20855543
Proteomics. 2018 Feb;18(3-4):
pubmed: 29327814
Pract Exp Adv Res Comput 2018 (2018). 2018 Jul;2018:
pubmed: 31598610
J Proteome Res. 2016 Aug 5;15(8):2422-32
pubmed: 27291504