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A critical element of mass spectrometry-based proteomics is to relate with high statistical significance experimental obtained tandem
mass spectrometry (MS/MS) data to peptide sequences from a protein database. Interestingly, among all fragment ions in MS/MS
spectra exists a subset of sequence specific complementary ion pairs (e.g. bn/ym-n, with m being the peptide length) of considerable
high reliability. Here, we investigated the reliability of complementary ion pairs formed in CAD and CAD/ETD MS/MS and developed
a reliability-based approach of intensification of these ion signals prior to database searching. Such intensification should afford higher
yield of peptide identification in database searching with Mascot. In a large-scale proteomics experiment using high-resolution orbitrap
MS, an increase in the number of peptide identifications was obtained relative to the original CAD MS/MS spectra when intensified
CAD/ETD complementary (+18.6%) and CAD complementary pairs (+17.2%) were submitted to the Mascot search engine. This
also exceeded the results obtained by deisotoping/deconvolution of CAD MS/MS spectra. Extending this approach afforded efficient
extraction of sequence specific complementary ions of co-isolated peptides. For all MS/MS spectra, a matrix was constructed to calculate
the sum of all combinations of possible complementary pairs corresponding to peptide monoisotopic masses present in close proximity
to the isolation window of the target peptide. After this, n+1 spectra were constructed, with n being the number of virtual spectra
comprising intensified complementary ions from co-isolated peptides. All together, these approaches demonstrated an impressive gain
of 42.4% more peptide identifications (p<0.05) compared to that of the CAD unprocessed data set.
Frank Kjeldsen (Chemistry, University of Southern Denmark (SDU), 2001: Ph.D., Biological Mass Spectrometry, SDU/Uppsala University, 2004)
has been an associate professor at SDU since 2009. After graduation he completed post-doctoral studies both at Uppsala University and later at
SDU. Frank has an extensive record of studying novel gas-phase ion-electron reactions and their application to biological mass spectrometry. In
his current position, he is focused on mass spectral interrogation, novel chemistries in proteomics and developing methodology and theory in mass
spectrometry with the goal of reaching in-depth protein and peptide characterization. He has published close to 50 papers in peer-review journals.
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