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Abstract No.: ThP-002
Session: Activation and Dissociation
Presentation date: Thu, Aug 31, 2006
Presentation time: 14:30 – 16:00

Structural Characterization of Peptides and Glycosylated Peptides: How Much Information Can We Get by Combining CID, IRMPD, and ECD?

Yayoi Hongo1, Takemichi Nakamura1, Akihiro Sato2

1 RIKEN, The Institute of Physical and Chemical Research, Wako,Saitama, Japan
2 Jasco International CO.,LTD., Hachioji,Tokyo, Japan

Correspondence address: Yayoi Hongo, RIKEN, The Institute of Physical and Chemical Research, Molecular Characterization Team, 2-1, Hirosawa, Wako,Saitama, 351-0198 Japan.

Keywords: Collision-Induced Dissociation (CID); Electron-Capture Dissociation; IRMPD; Peptide, Modified.

Novel aspect: Combining CID, IRMPD, and ECD to enhance capability of MS/MS for structural characterization of peptides and glycopeptides.


We examined various dissociation methods in order to establish how much structural information can be extracted from mass spectra of one peptide. Tandem mass spectrometry (MS/MS and MSn) have widely been used for protein identification and structural characterization of modified peptides, e.g. glycosylated and phosphorylated peptides. The advancement of MS/MS and MSn owes a lot to discovery, development, and implementation of a wide range of dissociation methods including low-energy collision induced dissociation (CID), infrared multiphoton dissociation (IRMPD), and electron capture dissociation (ECD). Each dissociation method has its own advantages and limitations. In biological applications, amino acid sequences and/or post-translational modifications often need to be characterized with minimal amount of samples in a high-throughput manner. In such case, particular dissociation method would be only choice in a number of occasions but good enough to get the information answering the biological question. On the other hand, it is an interesting challenge to analyze the structure of a particular molecule as detail as possible, solely by mass spectrometry but with every available fragmentation techniques. In this work, we have explored a strategy to get maximum structural information from peptides and glycopeptides by combining CID, IRMPD, and ECD rather than by using a single method.

An IonSpec QFT (quadrupole Fourier transform) mass spectrometer equipped with a nano-ESI source was used for CID, IRMPD, and ECD experiments. A triple quadrupole/ion trap mass spectrometer (4000 QTRAP, AppliedBiosystems) was also used for obtaining beam-type CID spectra. Standard peptides including substance P, [Glu1] fibrinopeptide, angiotensin I and angiotensin II were obtained from commercial sources. Glycosylated peptide samples were prepared from commercially available glycoproteins according to literatures.

Regular ECD gave very specific product ion spectra with c-z series dominant as already known. Whereas, ECD combined with IRMPD sometimes gave unique spectrum patterns containing neutral loss peaks, which did not appear in individual ECD or IRMPD spectrum. These observations indicate that the combination of two dissociation method can open additional fragmentation channels that were not accessible by individual dissociation method. The availability of new fragmentation channels may depend on amino acid sequences and/or gas-phase peptide conformations. The neutral loss fragmentation seems to occur at specific side chains. These points strongly suggest that the MS/MS analysis with combined dissociation methods would provide us more structural information when we analyze glycosylated and unmodified peptide.