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Tandem parallel fragmentation of peptides for mass spectrometry.
Anal Chem. 2006 Sep 15; 78(18):6391-7.AC

Abstract

Parallel fragmentations of peptides in the source region and in the collision cell of tandem mass spectrometers are sequentially combined to develop parallel collision-induced-dissociation mass spectrometry (p2CID MS). Compared to MS/MS spectra, the p2CID mass spectra show increased signal intensities (2-400-fold) and number of sequence ions. This improvement is attributed to the fact that p2CID MS virtually samples all the ions generated by electrospray ionization, including intact and fragment ions of different charge states from a peptide. We implement the method using a quadrupole time-of-flight tandem mass spectrometer. The instrument is operated in TOF-MS mode that allows the ions from source region broadband-passing the first mass analyzer to enter the collision cell. Cone voltage and collision energy are investigated to optimize the outcome of the two parallel CID processes. In the in-source parallel CID, elevated cone voltage produces singly charged intact peptide ions and large fragment ions, as well as decreases the charge-state distribution of peptide ions mainly to double and single charges. The in-collision-cell parallel CID is optimized to dissociate the ions from the source region to produce small and medium fragment ions. The method of p2CID MS is especially useful for sequencing of large peptides with labile amide bonds and peptides with C-terminal arginine. It has unique potential for de novo sequencing of peptides and proteome analysis, especially for affinity-enriched subproteomes.

Authors+Show Affiliations

Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

16970313

Citation

Ramos, Alexis A., et al. "Tandem Parallel Fragmentation of Peptides for Mass Spectrometry." Analytical Chemistry, vol. 78, no. 18, 2006, pp. 6391-7.
Ramos AA, Yang H, Rosen LE, et al. Tandem parallel fragmentation of peptides for mass spectrometry. Anal Chem. 2006;78(18):6391-7.
Ramos, A. A., Yang, H., Rosen, L. E., & Yao, X. (2006). Tandem parallel fragmentation of peptides for mass spectrometry. Analytical Chemistry, 78(18), 6391-7.
Ramos AA, et al. Tandem Parallel Fragmentation of Peptides for Mass Spectrometry. Anal Chem. 2006 Sep 15;78(18):6391-7. PubMed PMID: 16970313.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Tandem parallel fragmentation of peptides for mass spectrometry. AU - Ramos,Alexis A, AU - Yang,Hua, AU - Rosen,Lauren E, AU - Yao,Xudong, PY - 2006/9/15/pubmed PY - 2007/4/27/medline PY - 2006/9/15/entrez SP - 6391 EP - 7 JF - Analytical chemistry JO - Anal Chem VL - 78 IS - 18 N2 - Parallel fragmentations of peptides in the source region and in the collision cell of tandem mass spectrometers are sequentially combined to develop parallel collision-induced-dissociation mass spectrometry (p2CID MS). Compared to MS/MS spectra, the p2CID mass spectra show increased signal intensities (2-400-fold) and number of sequence ions. This improvement is attributed to the fact that p2CID MS virtually samples all the ions generated by electrospray ionization, including intact and fragment ions of different charge states from a peptide. We implement the method using a quadrupole time-of-flight tandem mass spectrometer. The instrument is operated in TOF-MS mode that allows the ions from source region broadband-passing the first mass analyzer to enter the collision cell. Cone voltage and collision energy are investigated to optimize the outcome of the two parallel CID processes. In the in-source parallel CID, elevated cone voltage produces singly charged intact peptide ions and large fragment ions, as well as decreases the charge-state distribution of peptide ions mainly to double and single charges. The in-collision-cell parallel CID is optimized to dissociate the ions from the source region to produce small and medium fragment ions. The method of p2CID MS is especially useful for sequencing of large peptides with labile amide bonds and peptides with C-terminal arginine. It has unique potential for de novo sequencing of peptides and proteome analysis, especially for affinity-enriched subproteomes. SN - 0003-2700 UR - https://www.unboundmedicine.com/medline/citation/16970313/Tandem_parallel_fragmentation_of_peptides_for_mass_spectrometry_ L2 - https://doi.org/10.1021/ac060672t DB - PRIME DP - Unbound Medicine ER -