Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

(E)-N′-[(E)-3-Phenyl­allyl­idene]benzo­hydrazide

In the title mol­ecule, C16H14N2O, the dihedral angle between the two phenyl rings is 23.5 (6)°. In the crystal, N—H—O hydrogen bonds link mol­ecules into chains running along the a axis

N-Methyl-3,5-dinitro­benzamide

The asymmetric unit of the title compound, C8H7N3O5, contains two independent mol­ecules in which the amide plane is oriented at dihedral angles of 29.82 (2) and 31.17 (2)° with respect to the benzene ring. In the crystal, mol­ecules are connected via inter­molecular N—H⋯O hydrogen bonds, forming chains running along the b axis

Temperature-dependent Mollow triplet spectra from a single quantum dot: Rabi frequency renormalisation and sideband linewidth insensitivity

We investigate temperature-dependent resonance fluorescence spectra obtained from a single self-assembled quantum dot. A decrease of the Mollow triplet sideband splitting is observed with increasing temperature, an effect we attribute to a phonon-induced renormalisation of the driven dot Rabi frequency. We also present first evidence for a non-perturbative regime of phonon coupling, in which the expected linear increase in sideband linewidth as a function of temperature is cancelled by the corresponding reduction in Rabi frequency. These results indicate that dephasing in semiconductor quantum dots may be less sensitive to changes in temperature than expected from a standard weak-coupling analysis of phonon effects.Comment: Close to published version, new figure and minor changes to the text. 5 pages, 3 figure

1,4-Bis(2-pyridylmethyl­eneamino­meth­yl)benzene

The asymmetric unit of the centrosymmetric title compound, C20H18N4, contains one half-mol­ecule. The pyridine and benzene rings are oriented at a dihedral angle of 77.21 (7)°