title: Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling.
abstract: In this study, we have implemented a new quality control (QC) parameter for peptide profiling based on isotopic distributions. This QC parameter is an objective measure and facilitates automatic sorting of large numbers of peptide spectra. Peptides in human serum samples were enriched using reversed-phase C(18)-functionalized magnetic beads using a high-throughput robotic platform. High-resolution MALDI-TOF and ultrahigh resolution MALDI-FTICR mass spectra were obtained and a workflow was developed for automated analysis and evaluation of these profiles. To this end, the isotopic distributions of multiple peptides were quantified from both MALDI-TOF and MALDI-FTICR spectra. Odd peptide isotope distributions in TOF spectra could be rationalized from ultrahigh resolution FTICR spectra that showed overlap of different peptides. The comparison of isotope patterns with estimated polyaveragine distributions was used to calculate a QC value for each single mass spectrum. Sorting these QC values enabled the best MALDI spectrum to be selected from replicate spots. Moreover, using this approach spectra containing high intensities of polymers or other contaminants and lacking peptides of interest can be efficiently removed from a clinical dataset. In general, this method simplifies the exclusion of low quality spectra from further statistical analysis.
authors.affiliation: Department of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Simone
authors.initials: S
authors.lastname: Nicolardi
authors.forename: Magnus
authors.initials: M
authors.lastname: Palmblad
authors.forename: Hans
authors.initials: H
authors.lastname: Dalebout
authors.forename: Marco
authors.initials: M
authors.lastname: Bladergroen
authors.forename: Rob A E M
authors.initials: RA
authors.lastname: Tollenaar
authors.forename: André M
authors.initials: AM
authors.lastname: Deelder
authors.forename: Yuri E M
authors.initials: YE
authors.lastname: van der Burgt
mesh_terms: D001798:Blood Proteins / Q000032:analysis*; D005583:Fourier Analysis; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D007554:Isotopes / Q000737:chemistry; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry*; D011786:Quality Control; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D001798:Blood Proteins; D007554:Isotopes; D010455:Peptides