scholarly journals Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry

2004 ◽  
Vol 20 (12) ◽  
pp. 1948-1954 ◽  
Author(s):  
Y. Fu ◽  
Q. Yang ◽  
R. Sun ◽  
D. Li ◽  
R. Zeng ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Peptide Identification ◽  
Tandem Mass ◽  
Kernel Trick ◽  
Fragment Ions

A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST

PROTEOMICS ◽  
2004 ◽  
Vol 4 (4) ◽  
pp. 961-969 ◽  
Author(s):  
Jane Razumovskaya ◽  
Victor Olman ◽  
Dong Xu ◽  
Edward C. Uberbacher ◽  
Nathan C. VerBerkmoes ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Peptide Identification ◽  
Computational Method ◽  
Mass Spectrometry Analysis ◽  
Tandem Mass ◽  
Spectrometry Analysis ◽  
Tandem Mass Spectrometry Analysis

scholarly journals Analysis of the Core Oligosaccharide ofAeromonas hydrophila(Chemotype III) Lipopolysaccharide Using Fast Atom Bombardment, Electrospray and Low Energy Tandem Mass Spectrometry

1994 ◽  
Vol 12 (2) ◽  
pp. 55-68 ◽  
Author(s):  
Joseph Banoub ◽  
Emmanuel Gentip ◽  
Derek H. Shaw
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Fast Atom Bombardment ◽  
Low Energy ◽  
Tandem Mass ◽  
Core Oligosaccharide ◽  
Molecular Ion ◽  
The Core ◽  
Fragment Ions ◽  
Positive Ion

Fast-atom bombardment mass spectrometry (FAB-MS) was employed for the structural analysis of the core oligosaccharide ofAeromonas hydrophila(Chemotype III) lipopolysaccharide. Positive ion FAB-MS of the underivatized core oligosaccharide gave the protonated molecular ion, confrrming the correct composition in terms of hexoses, heptoses and Kdo which was present as a bicyclic furanosidic lactone. Negative ion FAB-MS gave the deprotonated molecular ion and fragment ions which were derived from more than two cleavage events with charge retention at the reducing and non-reducing terminals. Positive ion F AB-MS of the permethylated core oligosaccharide afforded fragment ions consistent with the defined sequence and branching patterns of the sugar constituents. The electrospray mass spectrum (ESMS) in the positive ion mode of the underivatized core oligosaccharide afforded the protonated molecular ion in the singly and doubly charged forms. Low energy collision-activated dissociation tandem mass spectrometry (CAD MS/MS) analysis of the protonated molecular ion [M+2H]+2provided additional structural data. ESMS of the permethylated and N-acetylated permethylated core oligosaccharides provided useful structural indices and afforded a characteristic pattern for fragmentions resulting from the opening of the methylated bicyclic Kdo furanosidic 1,7- lactone, which was similar to that obtained in the corresponding FAB-MS.

Characterization of Oligosaccharides of the Lactosamine Series Derived from Keratan Sulfates by Tandem Mass Spectrometry

2000 ◽  
Vol 6 (2) ◽  
pp. 193-203 ◽  
Author(s):  
Masayuki Kubota ◽  
Keiichi Yoshida ◽  
Akira Tawada ◽  
Mamoru Ohashi
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Bond Cleavage ◽  
The Other ◽  
Negative Ion ◽  
Ring Cleavage ◽  
Tandem Mass ◽  
Fragment Ions ◽  
Glycosidic Bond Cleavage

Positive- and negative-ion fast-atom bombardment tandem mass spectrometry with collision-induced dissociation (FAB-CID-MS/MS) has been used in the characterization of di-and tetra-saccharides of the lactosamine series from keratan sulfates. FAB-CID-MS/MS of Galβ1-4GlcNAc (L1) exhibited strong fragment ions originating from ring cleavage at the reducing-terminal sugar moiety together with glycosidic bond-cleavage ions, whereas GlcNAcβ1-3Gal (K1) showed strong glycosidic bond-cleavage ions but no ring-cleavage ions. A series of ring-cleavage fragment ions was observed with members of the L-series which have free hydroxyl groups at the C1 and C3 positions. CID-MS/MS spectra of the [M + Na – SO3]+ ion ( m/z 406) from L2 and the [M + Na − 2SO3]+ ion ( m/z 406) from L4 were almost identical with the CID-MS/MS spectrum of the [M + Na]+ ion ( m/z 406) from L1, which indicated that the sugar skeletons of L2 and L4 are the same as that of L1. On the other hand, the CID-MS/MS spectrum of the [M + Na – SO3]+ ion ( m/z 508) from L4 did not resemble that of the [M + Na]+ ion ( m/z 508) from L2. The former showed peaks that were additional to the peaks in the latter. Since these extra peaks were accounted for on the basis of the structure of L3 [Galβ1(6S)-4GlcNAc, S = sulfate], the in-source loss of sulfate groups by ester exchange upon FAB ionization takes place in a dual manner; one reaction at the non-reducing terminal sugar to give L2 and the other at the reducing-terminal sugar to give L3. The CID-MS/MS spectra were characteristic for the tetrasaccharides L1-L1, L2-L2 and L4-L4 while in-source fragmentation confirms the component disaccharides of each tetrasaccharide. The structure of a tetrasaccharide trisulfate was confirmed as L2–L4 and not L4–L2 by CID-MS/MS. Negative-ion FAB-CID-MS/MS spectra of the sulfated di-and tetra-saccharides showed a pattern similar to that of the positive-ion spectra. Subtraction of the CID-MS/MS spectrum of the [M – H]− ion of L2 [Galβ1-4GlcNAc(6S)] from that of the [M – H – SO3]− ion of L4 [Gal(6S)β1-4GlcNAc(6S)] gave several specific ions whose origins were nicely explained on the basis of the structure of L3. The structure of a pentasaccharide consisting of N-acetylneuraminic acid and a tetrasaccharide trisulfate was confirmed, on the basis of FAB-CID-MS/MS, as NeuNAcα2-6L2-L4.

Optimization of pyrolysis–desorption chemical ionization mass spectrometry and tandem mass spectrometry of polysaccharides

1994 ◽  
Vol 72 (2) ◽  
pp. 345-351 ◽  
Author(s):  
R.J. Helleur ◽  
Pierre Thibault
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Chemical Ionization ◽  
Operating Conditions ◽  
High Mass ◽  
Chemical Ionization Mass Spectrometry ◽  
Ionization Mass ◽  
Tandem Mass ◽  
Mass Fragment ◽  
Fragment Ions

The operating conditions for pyrolysis–desorption ammonia chemical ionization mass spectrometry and tandem mass spectrometry have been optimized and the technique evaluated for the production and analysis of structurally-informative pyrolytic fragmentation ions corresponding to intact anhydrohexose oligosaccharides, using amylose as the model polysaccharide. Among the various parameters examined it was found that the nature of the solvent used to adhere the sample to the emitter coil and the configuration of the emitter and the rate at which it is heated all play important roles in determining the efficiency of the pyrolytic process and the production of high mass fragment ions. Adjustment of reagent gas pressure together with source temperature also influence the chemical integrity of high mass oligomeric pyrolysis products. Under optimal operating conditions using ammonia reagent gas, the analyses of cellulose, laminarin, agars, and chitin gave relatively abundant ions corresponding to ammonium (or protonated) adducts of up to anhydrohexose tetrasaccharide. More importantly, the generation of such higher mass fragment ions provided a sustained ionic current of sufficient duration to perform tandem mass spectrometric analyses.

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