SWEET SOFTWARE FOR BIOSCIENCES
Applied Numerics develops and hosts software for glycan and glycopeptide mass spectrometry data analysis.
SOFTWARE AS A SERVICE
Glycopeptide Identification with CID MS2 spectra.
GlycopeptideID is a web tool developed to identify intact glycopeptides. The emphasis is on resolving the combined complexity of an unknown peptide and glycan. Peptides are identified by matching the MS2 spectra against a protein database and the glycans against a glycan database or de novo glycans. The peptides can be form a single protein or from the whole UniProt DB with given taxonomy. For details see the glycopeptideID poster and the documentation of the GlycopeptideID open access web tool.
GlycopeptideID is provided in two forms
- an open access web tool for small scale analyses in return for user feedback which will be used by Applied Numerics to improve and further develop the software.
- for researchers with large amounts of data and requiring guaranteed uptime, annual subscription based access to GlycopeptideID is also available via a dedicated large server or a cluster in the Amazon AWS computing cloud.
Glycan profiling and identification with LC-MS-MS2 data.
GlycanID is a library of software methods developed for semi-quantitative LC-MS-MS2 profiling and identification of glycans. The glycan profile is based on LC-MS features generated with feature detection and alignment tools developed for proteomics. Glycans are identified at the composition level and the identification is based on matching the MS2 or MS data against a glycan composition database or de novo glycans. The emphasis is on resolving the potential complexity caused by different charge states, adduct combinations, contaminants and possible in-source decay.
PUBLICATIONS AND DOCUMENTATION
Scientific Papers
Peltoniemi, H., Natunen, S., Ritamo, I., Valmu, L., Räbinä, J. (2013). Novel data analysis tool for semiquantitative LC-MS-MS2 profiling of N-glycans. Glycoconjugate Journal, 2013, Volume 30, Issue 2, pp 159-170 (Abstract)
Peltoniemi H., Joenväärä S., Renkonen R. (2009). De novo glycan structure search with CID MS/MS spectra of native N-glycopeptides. Glycobiology. 2009. 19:707-714. (Abstract)
Joenväärä, S. et al., N-Glycoproteomics – an automated workflow approach.,
Glycobiology 2008 18(4):339-349
Posters
Web tool for N-glycopeptide identification with CID MS2 spectra (pdf), presented at HUPO 2014
Automated N-Glycan Composition Analysis with LC-MS/MSMS (pdf), presented at HUPO 2009
De novo glycan structure search with CID MS/MS spectra of native N-glycopeptides (pdf), presented at HUPO 2008
Other publication
Peltoniemi, H., Ritamo, I., Räbinä, J. and Valmu, L., Automated N-Glycan Composition Analysis with LC-MS/MSMS, Glyco-Bioinformatics –Bits ‘n’ Bytes of Sugars, October 4th –8th , 2009, Potsdam, Germany (www.beilstein-institut.de/download/607/04_peltomieni.pdf)
De novo glycan structure search with CID MS/MS spectra of native N-glycopeptides (PowerPoint), presented at symposium: Glycoproteomics and glycolipidomics – with special reference to mass spectrometry. Haartman Institute, 2008.
Scientific papers using the methods developed by Applied Numerics
Kontro H., Joenväärä S., Haglund C., Renkonen R., Comparison of sialylated N-glycopeptide levels in serum of pancreatic cancer patients, acute pancreatitis patients, and healthy controls. Proteomics. 2014 Aug;14(15):1713-23.
Ritamo I., Cloutier M., Valmu L., Néron S., Räbinä J., Comparison of the glycosylation of in vitro generated polyclonal human IgG and therapeutic immunoglobulins. Mol Immunol. 2014 Feb;57(2):255-62.
Natunen S., Lampinen M., Suila H., Ritamo I., Pitkänen V., Nairn A.V., Räbinä J., Laitinen S., Moremen K.W., Reutter W., Valmu L., Metabolic glycoengineering of mesenchymal stromal cells with N-propanoylmannosamine. Glycobiology. 2013 Aug;23(8):1004-12.
Ritamo I., Räbinä J., Natunen S., Valmu L., Nanoscale reversed-phase liquid chromatography-mass spectrometry of permethylated N-glycans. Anal Bioanal Chem. 2013 Mar;405(8):2469-80.
CONTACT
Hannu Peltoniemi
Hannu Peltoniemi, Founder and CEO, has two decades experience of computational software development for solving practical problems in several application areas, including bio-informatics and systems biology.
Applied Numerics Ltd
Nuottapolku 10 A8
FI-00330 Helsinki, Finland
Phone +358503627125