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Goetze"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Nuclear and cytoplasmic fraction","Drosophila melanogaster","Kc167 cells"],"full_dataset_link":["http://www.ebi.ac.uk/pride/archive/projects/PXD000730"],"tissue":["Cell Culture"],"sample_protocol":["Drosophila KC 167 cells were fractionated into cytoplasmic/nuclear fractions using cytoskeleton buffer ((CSK): 10mM PIPES, 300mM Sucrose, 100mM NaCl, 3mM MgCl2, 1mM EGTA) and douncing. Nucelar extracts were further porcessed in digestion buffer (10 mM PIPES, 1 mM EGTA, 50 mM NaCl, 3 mM MgCl2, DNAse) . After digestion 250 mM ammonium sulfate was added for protein extraction. After tryptic digestion peptides were fractionated using strong cation exchange chromatography (SXC) (Nat Biotechnol. 2007 May;25(5):576-83. Epub 2007 Apr 22)"],"repository":["Pride"],"quantification_method":["Not available"],"modification":["iodoacetamide derivatized residue","monohydroxylated residue","acetylated residue"],"data_protocol":["MS2 spectra were searched with TURBOSequest (v27) against the ENSEMBL fly protein database release v27.3c. PSMs were post-processed with PeptideProphet and only peptides equal to or above a PeptideProphet threshold of p >= 0.9 (corresponding to an FDR around 3% at the spectrum level) were considered further. As above, the Drosophila dataset was post-processed to remove shared peptides and to conform to a rank compatible format."],"omics_type":["Proteomics"],"labhead":["Erich Brunner"],"instrument_platform":["LTQ"],"labhead_affiliation":["Institute of Molecular Life Sciences, University of Zurich, Switzerland"],"submission_type":["PARTIAL"],"species":["Drosophila Melanogaster (fruit Fly)"],"submitter_mail":["sgoetze@ethz.ch"],"publication":["24878426 Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH. Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. J Proteomics. 2014 108:269-283 10.1016/j.jprot.2014.05.011"],"curator_keywords":["Prime-xs project","Technical"],"submitter_affiliation":["Institute of Molecular Systems BiologySwiss Federal Institute of Technology Zurich (ETH)Auguste-Piccard.Hof 1CH-8093 Zürich"],"submitter_country":["Switzerland"],"pubmed_abstract":["The in silico prediction of the best-observable \"proteotypic\" peptides in mass spectrometry-based workflows is a challenging problem. Being able to accurately predict such peptides would enable the informed selection of proteotypic peptides for targeted quantification of previously observed and non-observed proteins for any organism, with a significant impact for clinical proteomics and systems biology studies. Current prediction algorithms rely on physicochemical parameters in combination with positive and negative training sets to identify those peptide properties that most profoundly affect their general detectability. Here we present PeptideRank, an approach that uses learning to rank algorithm for peptide detectability prediction from shotgun proteomics data, and that eliminates the need to select a negative dataset for the training step. A large number of different peptide properties are used to train ranking models in order to predict a ranking of the best-observable peptides within a protein. Empirical evaluation with rank accuracy metrics showed that PeptideRank complements existing prediction algorithms. Our results indicate that the best performance is achieved when it is trained on organism-specific shotgun proteomics data, and that PeptideRank is most accurate for short to medium-sized and abundant proteins, without any loss in prediction accuracy for the important class of membrane proteins.