NDLI: Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

Content Provider	Springer Nature Link
Author	Oberacher, Herbert Mayr, Bettina M. Huber, Christian G.
Copyright Year	2004
Abstract	We present the first global computer-aided sequencing algorithm for the de novo determination of short nucleic acid sequences. The method compares the fragment ion spectra generated by collision-induced dissociation of multiply charged oligodeoxynucleotide-ions to the m/z values predicted employing established fragmentation pathways from a known reference sequence. The closeness of matching between the measured spectrum and the predicted set of fragment ions is characterized by the fitness, which takes into account the difference between measured and predicted m/z values, the intensity of the fragment ions, the number of fragments assigned, and the number of nucleotide positions not covered by fragment ions in the experimental spectrum. Smaller values for the fitness indicate a closer match between the measured spectrum and predicted m/z values. In order to find the sequence most closely matching the experimental spectrum, starting from a given nucleotide composition all possible oligonucleotide sequences are assembled followed by identification of the correct sequence by the lowest fitness value. Using this concept, sequences of 5- to 12-mer oligodeoxynucleotides were successfully de novo determined. High sequence coverage with fragment ions was essential for obtaining unequivocal sequencing results. Moreover, the collision energy was shown to have an impact on the interpretability of tandem mass spectra by the de novo sequencing algorithm. Experiments revealed that the optimal collision energy should be set to a value just sufficient for complete fragmentation of the precursor ion.
Starting Page	32
Ending Page	42
Page Count	11
File Format	PDF
ISSN	10440305
Journal	Journal of The American Society for Mass Spectrometry
Volume Number	15
Issue Number	1
e-ISSN	18791123
Language	English
Publisher	Springer-Verlag
Publisher Date	2004-01-01
Publisher Institution	The American Society for Mass Spectrometry
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Analytical Chemistry Biotechnology Organic Chemistry Proteomics Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Structural Biology

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

De novo sequencing of peptides on single resin beads by MALDI-FTICR tandem mass spectrometry

Novor: Real-Time Peptide de Novo Sequencing Software

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Liquid chromatography—tandem mass spectrometry analysis of the DNA adducts of aristolochic acids

Rapid discrimination of archaeal tetraether lipid cores by liquid chromatography-tandem mass spectrometry

“De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study

Enhancing the response of alkyl methylphosphonic acids in negative electrospray ionization liquid chromatography tandem mass spectrometry by post-column addition of organic solvents

Determination of steroids by liquid chromatography/mass spectrometry

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

Similar Documents

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry

De novo sequencing of peptides on single resin beads by MALDI-FTICR tandem mass spectrometry

Novor: Real-Time Peptide de Novo Sequencing Software

Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Liquid chromatography—tandem mass spectrometry analysis of the DNA adducts of aristolochic acids

Rapid discrimination of archaeal tetraether lipid cores by liquid chromatography-tandem mass spectrometry

“De novo” peptide sequencing by MALDI-quadrupole-ion trap mass spectrometry: A preliminary study

Enhancing the response of alkyl methylphosphonic acids in negative electrospray ionization liquid chromatography tandem mass spectrometry by post-column addition of organic solvents

Determination of steroids by liquid chromatography/mass spectrometry

Automated de novo sequencing of nucleic acids by liquid chromatography-tandem mass spectrometry