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February 2011

Volume 10Issue 2S1-S11
Open Access
On the cover:A new multi-capillary inlet and dual electrodynamic ion funnel interface coupled to a triple quadrupole mass spectrometer significantly enhances the efficiency of ion transmission and the overall sensitivity and limits of detection for targeted selected reaction monitoring (SRM) mass spectrometry based quantification. For details, see article by Mahmud Hossain et al., pages M000062-MCP201, 1–9. A novel crosslinker CBDPS which combines three features for the MS analysis of the peptide crosslinks: isotopic coding, CID cleavage, and biotin affinity tagging. These features ensure effective enrichment, confident detection, rapid automated crosslink-type determination, and identification of the individual peptides composing each inter-peptide crosslink. For details, see article by Evgeniy V. Petrotchenko et al., pages M110.001420, 1–8. Novel solvent free matrix deposition methods allow high spatial resolution MALDI imaging mass spectrometry of phospholipids from tissue sections. In combination with progress in MS instrumentation, these allow imaging MS on different length scales, from whole body down to cellular dimensions. For details, see article by Pierre Chaurand et al., pages O110.004259, 1–11. A recent development of the selected reaction monitoring technique, performed on triple quadrupole instruments, increases drastically the number of peptides measured in a single targeted proteomics experiment, thus opening new avenues towards comprehensive proteome analysis. The intelligent prioritization of the SRM measurements results in increased sensitivity, throughput, and precision. In such an experiment, a small set of primary transitions is measured for quantification, while they concomitantly trigger the acquisition of an expanded set of SRM transitions for identity confirmation. For details, see article by Reiko Kiyonami et al., pages M110.002931, 1–11. A fully-integrated proteomics sample processing and analysis platform, termed rare cell proteomic reactor (RCPR), was developed for large-scale quantitative proteomic analysis of hESCs with approximately 50,000 cells. A ready-to-use and chemically defined medium and an in situ differentiation procedure were developed for complete SILAC-labeling of hESCs with well-characterized self-renewal and differentiation properties. For details, see article by Ruijun Tian et al., M110.000679 pages 1–10. Immunoaffinity mass spectrometry involving the use of peptide-specific antibodies vs. the use of Triple X Proteomics antibodies (shaded in grey). Compared to classical peptide-specific antibodies with one-analyte specificity, TXP antibodies are generated with targeted multi-specificity capable of capturing peptide subsets that share the same terminus. For details, see article by Sibylle Hoeppe et al., pages M110.002857, 1–11. High pressure digestion combined with intact protein HPLC enables the integration of top-down and bottom-up proteomics for more complete characterization of protein isoforms arising from posttranslational modifications. For details, see article by Daniel López-Ferrer et al., pages M110.001479, 1–11....
On the cover:A new multi-capillary inlet and dual electrodynamic ion funnel interface coupled to a triple quadrupole mass spectrometer significantly enhances the efficiency of ion transmission and the overall sensitivity and limits of detection for targeted selected reaction monitoring (SRM) mass spectrometry based quantification. For details, see article by Mahmud Hossain et al., pages M000062-MCP201, 1–9. A novel crosslinker CBDPS which combines three features for the MS analysis of the peptide crosslinks: isotopic coding, CID cleavage, and biotin affinity tagging. These features ensure effective enrichment, confident detection, rapid automated crosslink-type determination, and identification of the individual peptides composing each inter-peptide crosslink. For details, see article by Evgeniy V. Petrotchenko et al., pages M110.001420, 1–8. Novel solvent free matrix deposition methods allow high spatial resolution MALDI imaging mass spectrometry of phospholipids from tissue sections. In combination with progress in MS instrumentation, these allow imaging MS on different length scales, from whole body down to cellular dimensions. For details, see article by Pierre Chaurand et al., pages O110.004259, 1–11. A recent development of the selected reaction monitoring technique, performed on triple quadrupole instruments, increases drastically the number of peptides measured in a single targeted proteomics experiment, thus opening new avenues towards comprehensive proteome analysis. The intelligent prioritization of the SRM measurements results in increased sensitivity, throughput, and precision. In such an experiment, a small set of primary transitions is measured for quantification, while they concomitantly trigger the acquisition of an expanded set of SRM transitions for identity confirmation. For details, see article by Reiko Kiyonami et al., pages M110.002931, 1–11. A fully-integrated proteomics sample processing and analysis platform, termed rare cell proteomic reactor (RCPR), was developed for large-scale quantitative proteomic analysis of hESCs with approximately 50,000 cells. A ready-to-use and chemically defined medium and an in situ differentiation procedure were developed for complete SILAC-labeling of hESCs with well-characterized self-renewal and differentiation properties. For details, see article by Ruijun Tian et al., M110.000679 pages 1–10. Immunoaffinity mass spectrometry involving the use of peptide-specific antibodies vs. the use of Triple X Proteomics antibodies (shaded in grey). Compared to classical peptide-specific antibodies with one-analyte specificity, TXP antibodies are generated with targeted multi-specificity capable of capturing peptide subsets that share the same terminus. For details, see article by Sibylle Hoeppe et al., pages M110.002857, 1–11. High pressure digestion combined with intact protein HPLC enables the integration of top-down and bottom-up proteomics for more complete characterization of protein isoforms arising from posttranslational modifications. For details, see article by Daniel López-Ferrer et al., pages M110.001479, 1–11.

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