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Label-free quantitation of proteins analyzed by tandem mass spectrometry uses either integrated peak intensity from the parent-ion mass analysis (MS1) or features from fragment-ion analysis (MS2), such as spectral counts or summed fragment-ion intensity. We directly compared MS1 and MS2 quantitation by analyzing human protein standards diluted into Escherichia coli extracts on an Orbitrap mass spectrometer. We found that summed MS2 intensities were nearly as accurate as integrated MS1 intensities, and both outperformed MS2 spectral counting in accuracy and linearity. We compared these results to those obtained from two low-resolution ion-trap mass spectrometers; summed MS2 intensities from LTQ and LTQ Velos instruments were similar in accuracy to those from the Orbitrap. Data from all three instruments are available via ProteomeXchange with identifier PXD000602. Abundance measurements using MS1 or MS2 intensities had limitations, however. While measured protein concentration was on average well-correlated with the known concentration, there was considerable protein-to-protein variation. Moreover, not all human proteins diluted to a mole fraction of 10(-3) or lower were detected, with a strong falloff below 10(-4) mole fraction. These results show that MS1 and MS2 intensities are simple measures of protein abundance that are on average accurate but should be limited to quantitation of proteins of intermediate to higher fractional abundance.

Hair bundles of the inner ear have a specialized structure and protein composition that underlies their sensitivity to mechanical stimulation. Using mass spectrometry, we identified and quantified >1,100 proteins, present from a few to 400,000 copies per stereocilium, from purified chick bundles; 336 of these were significantly enriched in bundles. Bundle proteins that we detected have been shown to regulate cytoskeleton structure and dynamics, energy metabolism, phospholipid synthesis and cell signaling. Three-dimensional imaging using electron tomography allowed us to count the number of actin-actin cross-linkers and actin-membrane connectors; these values compared well to those obtained from mass spectrometry. Network analysis revealed several hub proteins, including RDX (radixin) and SLC9A3R2 (NHERF2), which interact with many bundle proteins and may perform functions essential for bundle structure and function. The quantitative mass spectrometry of bundle proteins reported here establishes a framework for future characterization of dynamic processes that shape bundle structure and function.

A major challenge for core facilities is determining quantitative protein differences across complex biological samples. Although there are numerous techniques in the literature for relative and absolute protein quantification, the majority is nonroutine and can be challenging to carry out effectively. There are few studies comparing these technologies in terms of their reproducibility, accuracy, and precision, and no studies to date deal with performance across multiple laboratories with varied levels of expertise. Here, we describe an Association of Biomolecular Resource Facilities (ABRF) Proteomics Research Group (PRG) study based on samples composed of a complex protein mixture into which 12 known proteins were added at varying but defined ratios. All of the proteins were present at the same concentration in each of three tubes that were provided. The primary goal of this study was to allow each laboratory to evaluate its capabilities and approaches with regard to: detection and identification of proteins spiked into samples that also contain complex mixtures of background proteins and determination of relative quantities of the spiked proteins. The results returned by 43 participants were compiled by the PRG, which also collected information about the strategies used to assess overall performance and as an aid to development of optimized protocols for the methodologies used. The most accurate results were generally reported by the most experienced laboratories. Among laboratories that used the same technique, values that were closer to the expected ratio were obtained by more experienced groups.

In a sense, the field of snake venom proteomics has been under investigation since the very earliest biochemical studies where it was soon recognized that venoms are comprised of complex mixtures of bioactive molecules, most of which are proteins. Only with the re-emergence of 2D polyacrylamide gel electrophoresis (2D PAGE) and the recent developments in mass spectrometry for the identification/characterization of proteins coupled with venom gland transcriptomes has the field of snake venom proteomics began to flourish and provide exciting insights into the protein composition of venoms and subsequently their pathological activities. In this manuscript we will briefly discuss the state of snake venom proteomics followed by the presentation of several straightforward experiments designed to explore approaches to investigating venom proteomics. The first set of experiments used 1D gel electrophoresis (1D PAGE) of Crotalus atrox venom followed by slice-by-slice analysis of the proteins using liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS). In the second set of experiments, C. atrox and Bothrops jararaca venoms were subjected to in-solution digestion followed by Fourier transform ion cyclotron resonance (FTICR) LC/MS/MS. The peptide ion-maps of these venoms were compared along with the proteins identified. In addition, the results were compared to the results observed from the 1D PAGE approach. From these studies it is clear that sample de-complexation/fractionation before mass spectrometry is still the best approach for maximum proteome coverage. Furthermore, comparison of venom proteomes based on tryptic peptide identities between the proteomes is not particularly effective since there does not appear to be a sufficient number of such identical peptides, derived from related proteins, present in venoms. Finally, as has previously been recognized without either better databases of venom protein sequences or facile and rapid de novo sequencing technologies for mass spectrometry, snake venom proteome investigation will remain a laborious task.