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Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification.
J Proteome Res. 2006 Aug; 5(8):1967-78.JP

Abstract

Mass spectrometric based sequencing of enzymatic generated peptides is widely used to obtain specific sequence tags allowing the unambiguous identification of proteins. In the present study, two types of desorption/ionization techniques combined with different modes of ion dissociation, namely vacuum matrix-assisted laser desorption/ionization (vMALDI) high energy collision induced dissociation (CID) and post-source decay (PSD) as well as atmospheric pressure (AP)-MALDI low energy CID, were applied for the fragmentation of singly protonated peptide ions, which were derived from two-dimensional separated, silver-stained and trypsin-digested hydrophilic as well as hydrophobic glomerular proteins. Thereby, defined properties of the individual fragmentation pattern generated by the specified modes could be observed. Furthermore, the compatibility of the varying PSD and CID (MS/MS) data with database search derived identification using two public accessible search algorithms has been evaluated. The peptide sequence tag information obtained by PSD and high energy CID enabled in the majority of cases an unambiguous identification. In contrast, part of the data obtained by low energy CID were not assignable using similar search parameters and therefore no clear results were obtainable. The knowledge of the properties of available MALDI-based fragmentation techniques presents an important factor for data interpretation using public accessible search algorithms and moreover for the identification of two-dimensional gel separated proteins.

Authors+Show Affiliations

Institute of Chemical Technologies and Analytics, Vienna University of Technology, A-1060 Vienna, Austria.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

16889419

Citation

Mayrhofer, Corina, et al. "Comparison of Vacuum Matrix-assisted Laser Desorption/ionization (MALDI) and Atmospheric Pressure MALDI (AP-MALDI) Tandem Mass Spectrometry of 2-dimensional Separated and Trypsin-digested Glomerular Proteins for Database Search Derived Identification." Journal of Proteome Research, vol. 5, no. 8, 2006, pp. 1967-78.
Mayrhofer C, Krieger S, Raptakis E, et al. Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification. J Proteome Res. 2006;5(8):1967-78.
Mayrhofer, C., Krieger, S., Raptakis, E., & Allmaier, G. (2006). Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification. Journal of Proteome Research, 5(8), 1967-78.
Mayrhofer C, et al. Comparison of Vacuum Matrix-assisted Laser Desorption/ionization (MALDI) and Atmospheric Pressure MALDI (AP-MALDI) Tandem Mass Spectrometry of 2-dimensional Separated and Trypsin-digested Glomerular Proteins for Database Search Derived Identification. J Proteome Res. 2006;5(8):1967-78. PubMed PMID: 16889419.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparison of vacuum matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI (AP-MALDI) tandem mass spectrometry of 2-dimensional separated and trypsin-digested glomerular proteins for database search derived identification. AU - Mayrhofer,Corina, AU - Krieger,Sigurd, AU - Raptakis,Emmanuel, AU - Allmaier,Günter, PY - 2006/8/8/pubmed PY - 2007/2/6/medline PY - 2006/8/8/entrez SP - 1967 EP - 78 JF - Journal of proteome research JO - J Proteome Res VL - 5 IS - 8 N2 - Mass spectrometric based sequencing of enzymatic generated peptides is widely used to obtain specific sequence tags allowing the unambiguous identification of proteins. In the present study, two types of desorption/ionization techniques combined with different modes of ion dissociation, namely vacuum matrix-assisted laser desorption/ionization (vMALDI) high energy collision induced dissociation (CID) and post-source decay (PSD) as well as atmospheric pressure (AP)-MALDI low energy CID, were applied for the fragmentation of singly protonated peptide ions, which were derived from two-dimensional separated, silver-stained and trypsin-digested hydrophilic as well as hydrophobic glomerular proteins. Thereby, defined properties of the individual fragmentation pattern generated by the specified modes could be observed. Furthermore, the compatibility of the varying PSD and CID (MS/MS) data with database search derived identification using two public accessible search algorithms has been evaluated. The peptide sequence tag information obtained by PSD and high energy CID enabled in the majority of cases an unambiguous identification. In contrast, part of the data obtained by low energy CID were not assignable using similar search parameters and therefore no clear results were obtainable. The knowledge of the properties of available MALDI-based fragmentation techniques presents an important factor for data interpretation using public accessible search algorithms and moreover for the identification of two-dimensional gel separated proteins. SN - 1535-3893 UR - https://www.unboundmedicine.com/medline/citation/16889419/Comparison_of_vacuum_matrix_assisted_laser_desorption/ionization__MALDI__and_atmospheric_pressure_MALDI__AP_MALDI__tandem_mass_spectrometry_of_2_dimensional_separated_and_trypsin_digested_glomerular_proteins_for_database_search_derived_identification_ L2 - https://doi.org/10.1021/pr060165s DB - PRIME DP - Unbound Medicine ER -