title: Influence of mass resolution on species matching in accurate mass and retention time (AMT) tag proteomics experiments.
abstract: Diverse mass spectrometric instruments have been used to provide data for accurate mass and retention time (AMT) tag proteomics analyses, including ion trap, quadrupole time-of-flight, and Fourier transform mass spectrometry (FTMS). An important attribute of these instruments, beside mass accuracy, is their spectral resolution. In fact, the ability to separate peaks with close m/z values is likely to play a major role in enabling species identification and matching in analyses of very complex proteomics samples. In FTMS, resolution is directly proportional to the detection period and can therefore be easily tuned. We took advantage of this feature to investigate the effect of resolution on species identification and matching in an AMT tag experiment. Using an Arabidopsis thaliana chloroplast protein extract as prototypical 'real-life' sample, we have compared the number of detected features, the optimal mass tolerance for species matching, the number of matched species and the false discovery rate obtained at various resolution settings. It appears that while the total number of matches is not significantly affected by a reduction of resolution in the range investigated, the confidence level of identifications significantly drops as evidenced by the estimated false discovery rate.
authors.affiliation: CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, 38054 Grenoble, France. christophe.masselon@cea.fr
authors.forename: Christophe D
authors.initials: CD
authors.lastname: Masselon
authors.forename: Sylvie
authors.initials: S
authors.lastname: Kieffer-Jaquinod
authors.forename: Sabine
authors.initials: S
authors.lastname: Brugière
authors.forename: Véronique
authors.initials: V
authors.lastname: Dupierris
authors.forename: Jérôme
authors.initials: J
authors.lastname: Garin
mesh_terms: D000465:Algorithms; D016477:Artifacts; D008970:Molecular Weight; D010449:Peptide Mapping / Q000379:methods*; D020543:Proteome / Q000032:analysis / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D021241:Spectrometry, Mass, Electrospray Ionization; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*
chemical_list: D020543:Proteome