An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

Combined Proteomics and Pathways Analysis of Collecting Duct Reveals a Protein Regulatory Network Activated in Vasopressin Escape

Low sensitivity is characteristic of many proteomics methods. Here we present an approach that combines proteomics based on “Difference Gel Electrophoresis” (DIGE) with bioinformatic pathways analysis to identify both abundant and relatively non-abundant proteins in inner medullary collecting duct (IMCD) altered in abundance during escape from vasopressin-induced antidiuresis. Rats received the vasopressin analog dDAVP by osmotic minipump plus either a daily water load (vasopressin escape) or only enough water to replace losses (control). Immunoblotting confirmed the hallmark of vasopressin escape, a decrease in aquaporin-2, and demonstrated a decrease in the abundance of the urea transporter UT-A3. DIGE identified 22 mostly high abundance proteins regulated during vasopressin escape. These proteins were analyzed using pathways analysis software to reveal protein clusters that include those identified by DIGE. A single dominant cluster emerged that included many relatively low abundance proteins (abundances too low for DIGE identification) including several transcription factors. Immunoblotting confirmed a decrease in total and phosphorylated c-myc, a decrease in c-fos, and increases in c-jun and p53. Furthermore, immunoblotting confirmed hypothesized changes in other proteins in the proposed network: increases in c-src, RACK1, calreticulin, and caspase 3, and decreases in SRC-1, Grp78/BiP, and annexin A4. This combined approach proved capable of uncovering regulatory proteins altered in response to a specific physiological perturbation without being directly detected by DIGE. The results demonstrate a dominant protein regulatory network in IMCD cells that is altered in association with vasopressin escape, providing a new framework for further studies of signaling in IMCD

Combined proteomics and pathways analysis of collecting duct reveals a protein regulatory network activated in vasopressin escape

Low sensitivity is characteristic of many proteomics methods. Presented here is an approach that combines proteomics based on difference gel electrophoresis (DIGE) with bioinformatic pathways analysis to identify both abundant and relatively nonabundant proteins in inner medullary collecting duct (IMCD) altered in abundance during escape from vasopressin-induced antidiuresis. Rats received the vasopressin analog dDAVP by osmotic minipump plus either a daily water load (vasopressin escape) or only enough water to replace losses (control). Immunoblotting confirmed the hallmark of vasopressin escape, a decrease in aquaporin-2, and demonstrated a decrease in the abundance of the urea transporter UT-A3. DIGE identified 22 mostly high-abundance proteins regulated during vasopressin escape. These proteins were analyzed using pathways analysis software to reveal protein clusters incorporating the proteins identified by DIGE. A single dominant cluster emerged that included many relatively low-abundance proteins (abundances too low for DIGE identification), including several transcription factors. Immunoblotting confirmed a decrease in total and phosphorylated c-myc, a decrease in c-fos, and increases in c-jun and p53. Furthermore, immunoblotting confirmed hypothesized changes in other proteins in the proposed network: Increases in c-src, receptor for activated C kinase 1, calreticulin, and caspase 3 and decreases in steroid receptor co-activator 1, Grp78/BiP, and annexin A4. This combined approach proved capable of uncovering regulatory proteins that are altered in response to a specific physiologic perturbation without being detected directly by DIGE. The results demonstrate a dominant protein regulatory network in IMCD cells that is altered in association with vasopressin escape, providing a new framework for further studies of signaling in IMCD

LC-MS/MS analysis of differential centrifugation fractions from native inner medullary collecting duct of rat

We carried out LC-MS/MS-based proteomic profiling of differential centrifugation fractions from rat inner medullary collecting duct (IMCD): 1) to provide baseline knowledge of the IMCD proteome and 2) to evaluate the utility of differential centrifugation in assessing trafficking of the water channel aquaporin-2 (AQP2). IMCD suspensions were freshly prepared from rat kidneys using standard methods. Homogenized samples were subjected to sequential centrifugations at 1,000, 4,000, 17,000, and 200,000 g. These samples, as well as the final supernatant, were subjected to LC-MS/MS analysis. Preliminary immunoblotting confirmed that the ratio of AQP2 in the 17,000-g fraction to the 200,000-g fraction underwent an increase in response to the vasopressin analog dDAVP, largely due to a reduction in the 200,000-g fraction. Immunoblotting for the major phosphorylated forms of AQP2 revealed that phosphorylated AQP2 was present in both the 17,000- and 200,000-g fractions. LC-MS/MS analysis showed that markers of “intracellular vesicles,” chiefly endosomal markers, were present in both the 17,000- and the 200,000-g fractions. In contrast, plasma membrane proteins were predominantly present in the 4,000- and 17,000-g fractions. Proteins associated with several multiprotein complexes (e.g., actin-related protein 2/3 complex and proteasome complex) were virtually exclusively present in the 200,000-g fraction. Overall, we identified 656 proteins, including 189 not previously present in the IMCD database. The data show that both the 17,000- and 200,000-g fractions are highly heterogeneous and cannot be equated with “plasma membrane” and “intracellular vesicle” fractions, respectively, leading us to propose an alternative approach for use of differential centrifugation to assess vesicular trafficking to the plasma membrane