On the Benefits of Acquiring Peptide Fragment Ions at High Measured Mass Accuracy.

@article{citeulike:2817272, abstract = {The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages.}, address = {Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.}, author = {Scherl, Alexander and Shaffer, Scott A A. and Taylor, Gregory K K. and Hernandez, Patricia and Appel, Ron D D. and Binz, Pierre-Alain A. and Goodlett, David R R. }, citeulike-article-id = {2817272}, doi = {10.1016/j.jasms.2008.02.005}, issn = {1044-0305}, journal = {Journal of the American Society for Mass Spectrometry}, keywords = {fdr, proteomics}, month = {March}, posted-at = {2008-05-20 18:47:01}, priority = {2}, title = {On the Benefits of Acquiring Peptide Fragment Ions at High Measured Mass Accuracy.}, url = {http://dx.doi.org/10.1016/j.jasms.2008.02.005}, year = {2008} }

TY - JOUR ID - citeulike:2817272 L3 - citeulike-article-id:2817272 TI - On the Benefits of Acquiring Peptide Fragment Ions at High Measured Mass Accuracy. JF - Journal of the American Society for Mass Spectrometry AD - Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA. SN - 1044-0305 N2 - The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages. KW - fdr KW - proteomics AU - Scherl, Alexander AU - Shaffer, Scott A AU - Taylor, Gregory K AU - Hernandez, Patricia AU - Appel, Ron D AU - Binz, Pierre-Alain AU - Goodlett, David R PY - 2008/03/04/ UR - http://dx.doi.org/10.1016/j.jasms.2008.02.005 ER -