Showing papers by "Jimmy K. Eng published in 2002"
TL;DR: Insights into the perturbative effects on genes involved in respiration, energy generation, and protein synthesis were obtained that would not have been apparent from measurements made at either the messenger RNA or protein level alone, illustrating the power of integrating different types of data obtained from the same sample for the comprehensive characterization of biological systems and processes.
702 citations
TL;DR: It is demonstrated that the combination of isotope coded affinity protein tags and multidimensional chromatography/mass spectrometry of tryptic peptide mixtures is capable of detecting and quantifying proteins of low abundance in complex samples.
Abstract: The effectiveness of proteome-wide protein identification and quantitative expression profiling is dependent on the ability of the analytical methodologies employed to routinely obtain information ...
311 citations
TL;DR: It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results, which reduces computer requirements and researcher efforts for analysis of the results.
Abstract: We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a com...
219 citations
Patent•
11 Sep 2002
TL;DR: In this paper, a method for correlating a peptide fragment mass spectrum with amino acid sequences derived from a database is provided, where the peptide is analyzed by a tandem mass spectrometer to yield a polygonal fragment spectrum, which is then compared with the experimentally derived fragment spectrum using a closeness-of-fit measure.
Abstract: A method for correlating a peptide fragment mass spectrum with amino acid sequences derived from a database is provided. A peptide is analyzed by a tandem mass spectrometer to yield a peptide fragment mass spectrum. A protein sequence database or a nucleotide sequence database is used to predict one or more fragment spectra for comparison with the experimentally-derived fragment spectrum. In one embodiment, sub-sequences of the sequences found on the database which define a peptide having a mass substantially equal to the mass of the peptide analyzed by the tandem mass spectrometer are identified as candidate sequences. For each candidate sequence, a plurality of fragments of the sequence are identified and the masses and m/z ratios of the fragments are predicted and used to form a predicted mass spectrum. The various predicted mass spectra are compared to the experimentally derived fragment spectrum using a closeness-of-fit measure, preferably calculated with a two-step process, including a calculation of a preliminary score end, for the highest-scoring predicted spectra, calculation of a correlation function.
1 citations
01 Jan 2002
TL;DR: In this article, the statistical occurrence of the six most common immonium ions observed in the QSTAR MS spectra was analyzed, as well as one negative control (D).
Abstract: Figure 2: A typical QSTAR MS spectra. Purple lines indicate immonium ion peaks. Overview Upon observing a high frequency of immonium ion in datasets run on the Qstar, the prospect of using these internal fragmentation peaks to improve peptide assignment probability seemed interesting. We analyzed the statistical occurrence of the six most common immonium ions observed in our dataset (H, I/L, F, V, Y, W), as well as one negative control (D). Methods • A total yeast extract from Saccharomyces cerevisiae (strain BY4741) was digested and separated into ten fractions using strong cation exchange.