Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling.

Mass spectrometry has become the method of choice for proteome characterization, including multicomponent protein complexes (typically tens to hundreds of proteins) and total protein expression (up to tens of thousands of proteins), in biological samples. Qualitative sequence assignment based on MS/MS spectra is relatively well-defined, while statistical metrics for relative quantification have not completely stabilized. Nonetheless, proteomics studies have progressed to the point whereby various gene-, pathway-, or network-oriented computational frameworks may be used to place mass spectrometry data into biological context.

Online nanoflow RP-RP-MS reveals dynamics of multicomponent Ku complex in response to DNA damage.

Tandem affinity purification (TAP) coupled with mass spectrometry has become the technique of choice for characterization of multicomponent protein complexes. While current TAP protocols routinely provide high yield and specificity for proteins expressed under physiologically relevant conditions, analytical figures of merit required for efficient and in-depth LC-MS analysis remain unresolved. Here we implement a multidimensional chromatography platform, based on two stages of reversed-phase (RP) separation operated at high and low pH, respectively.

Electronic spectroscopy and ultrafast energy relaxation pathways in the lowest Rydberg States of trimethylamine.

Resonance-enhanced multiphoton ionization photoelectron spectroscopy has been applied to study the electronic spectroscopy and relaxation pathways among the 3p and 3s Rydberg states of trimethylamine. The experiments used femtosecond and picosecond duration laser pulses at wavelengths of 416, 266, and 208 nm and employed two-photon and three-photon ionization schemes. The binding energy of the 3s Rydberg state was found to be 3.

Resolved: electronic states underneath broad absorptions.

The far UV absorption spectra of many polyatomic molecules show featureless, broad bands, even though the lifetimes of the underlying electronic states can be long enough to render the states observable. Using photoionization from Rydberg states we measure electron binding energies, thereby referencing the electronic spectra to the adiabatic ionization energy. In trimethylamine, we find that the 3s, the 3p(x,y), and the 3p(z) Rydberg states have binding energies of 3.

Rydberg fingerprint spectroscopy of hot molecules: structural dispersion in flexible hydrocarbons.

We explore how structural dispersion in flexible hydrocarbon chain molecules at very high temperatures is reflected in the photoionization spectra of Rydberg levels. The spectra of N,N-dimethylisopropanamine, N,N-dimethyl-1-butanamine, N,N-dimethyl-2-butanamine, N,N-dimethyl-3-hexanamine, and 1,4-dimethylpiperazine, taken at effective vibrational temperatures of 700-1000 K, show well-resolved features stemming from the 3p and 3s Rydberg states. The line shapes observed in molecules with internal rotation degrees of freedom show that multiple structures are populated.