Terry D. Lee

Qscore: an algorithm for evaluating SEQUEST database search results

A scoring procedure is described for measuring the quality of the results for protein identifications obtained from spectral matching of MS/MS data using the Sequest database search program. The scoring system is essentially probabilistic and operates by estimating the probability that a protein identification has come about by chance. The probability is based on the number of identified peptides from the protein, the total number of identified peptides, and the fraction of distinct tryptic peptides from the database that are present in the identified protein. The score is not strictly a probability, as it also incorporates information about the quality of the individual peptide matches. The result of using Qscore on a large test set of data was similar to that achieved using approaches that validate individual spectral matches, with only a narrow overlap in scores between identified proteins and false positive matches. In direct comparison with a published method of evaluating Sequest results, Qscore was able to identify an equivalent number of proteins without any identifiable false positive assignments. Qscore greatly reduces the number of Sequest protein identifications that have to be validated manually.

Composition and Functional Characterization of the Yeast Spliceosomal Penta-snRNP

Pre-mRNA introns are spliced in a macromolecular machine, the spliceosome. For each round of splicing, the spliceosome assembles de novo in a series of ATP-dependent steps involving numerous changes in RNA-RNA and RNA-protein interactions. As currently understood, spliceosome assembly proceeds by addition of discrete U1, U2, and U4/U6*U5 snRNPs to a pre-mRNA substrate to form functional splicing complexes. We characterized a 45S yeast penta-snRNP which contains all five spliceosomal snRNAs and over 60 pre-mRNA splicing factors. The particle is functional in extracts and, when supplied with soluble factors, is capable of splicing pre-mRNA. We propose that the spliceosomal snRNPs associate prior to binding of a pre-mRNA substrate rather than with pre-mRNA via stepwise addition of discrete snRNPs.

Rapid protein identification using a microscale electrospray LC/MS system on an ion trap mass spectrometer

A methodology has been developed for the rapid identification of gel separated proteins. Following in gel protein digestion with trypsin, the resulting peptide mixture is analyzed by on-line liquid chromatography, electrospray mass spectrometry (LC/MS). The mass spectral data containing either accurate mass values or sequence specific fragment ion information is then matched to a database of known protein sequences. Key features of the LC/MS system are the use of a novel integrated, microscale LC column-electrospray interface and variable flow solvent delivery to optimize the efficiency of sample loading and gradient elution. With these enhancements, only 10 min is required to analyze each sample. The method is routine for sample amounts ranging from 50 to 500 fmol. The analysis parameters for the ion trap mass spectrometer have to be carefully adjusted in order to keep pace with the rapidly eluting LC peaks. Although designed for rapid LC separations, the integrated column-electrospray interface is also able to provide extended analyses of selected components using a technique known as “peak parking. ”

Low flow high-performance liquid chromatography solvent delivery system designed for tandem capillary liquid chromatography-mass spectrometry

A solvent delivery system is described that is designed to increase the efficiency of liquid chromatography-mass spectrometry (LC/MS) analyses. Gradients formed by using two low pressure syringe pumps are stored in a length of narrow bore tubing (gradient loop) mounted on a standard high pressure switching valve. The preformed gradient is pushed through the column by using a high pressure syringe pump. The system is fully automated and can be controlled with either a personal computer or the mass spectrometer data system. Advantages include gradient operation without the use of split flows, pressure programed flow control for rapid sample loading and recycling to initial conditions, and a flow rate range of 0.1–20 μL/min, which is suitable for packed capillary columns 50–500 μm in diameter. The system has been used extensively for rapid molecular weight determinations of intact protein samples, as well as LC/MS and liquid chromatography-tandem mass spectrometry analyses of complex peptide mixtures.

Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures

The structural characterization of proteins and peptides isolated in minute quantities requires the most efficient use of available sample. A mass spectrometer data system was programmed to continuously evaluate incoming liquid chromatography/mass spectrometry data against a user-defined array of information. The resulting conclusions were used to automatically set and modify acquisition parameters in real time to collect collision-induced dissociation spectra for selected ions (tandem mass spectrometry). This approach has provided a mechanism to target specific subsets of masses in a complex mixture and/or to discriminate selectively against masses that are known or not of interest. Masses of contaminants or peptide masses derived from known proteins can be automatically recorded and removed from further consideration for collision-induced dissociation analysis. Once recorded, these “libraries” of masses can be used across multiple analyses. This technique directs the mass spectrometer data system to focus on the analysis of masses significant to the user, even if their signal intensities are well below the intensities of contaminating masses. When combined with a database search program to correlate tandem mass spectra to known protein sequences, the identity of the protein can be established unequivocally by using less than 100 fmol of sample.

Variable flow liquid chromatography-tandem mass spectrometry and the comprehensive analysis of complex protein digest mixtures

A microscale, variable flow, liquid chromatography-electrospray ionization source has been coupled to an ion trap mass spectrometer and used to analyze both simple and complex protein mixtures. By using an analytical technique described as “peak parking,” the sample analysis times for components eluting from a liquid Chromatograph can be greatly increased without sacrificing Chromatographic resolution. This was achieved by instantaneously reducing the column head pressure (and hence, flowrate) under peaks of interest to prolong their elution from the tip. With the technique, it is possible to perform manual parent ion selection, higher resolution narrow mass range scans, and multiple stages of tandem mass spectrometry (MS2 and MS3) within the context of a single eluting peak. Benefits normally associated with an off-line tandem mass spectrometry analysis, such as the optimization of collision induced dissociation parameters and the analysis of more than one charge state, can now be obtained with the increased sensitivity and selectivity afforded by the chromatography. The utility of this method for the comprehensive analysis of complex mixtures was illustrated with the analysis of an in-gel protein digest mixture derived from a single spot from a two-dimensional electrophoresis gel. In addition to the expected enzyme digestion products, other peptides derived from nonspecific cleavage by the enzyme and protein impurities, as well as those having oxidized, derivatized, or deamidated amino acid residues were fully characterized.

Differential Association of Hemoglobin with Proinflammatory High Density Lipoproteins in Atherogenic/Hyperlipidemic Mice A NOVEL BIOMARKER OF ATHEROSCLEROSIS

Studies in both mice and humans suggest that the anti- or proinflammatory nature of high density lipoprotein (HDL) may be a more sensitive predictor of risk for coronary heart disease events. In this study, we report the identification and characterization of two proteins (m/z 14,900 and 15,600) that are most dramatically associated with HDL in mouse models of atherosclerosis. Mass spectral analyses of proinflammatory HDL identified the two peaks to be hemoglobin (Hb) α and β chains, respectively, with no apparent post-translational modification. Biochemical analysis confirmed the differential association of Hb with HDL from hyperlipidemic mice. We further show that HDL-associated Hb is predominantly in the oxyHb form with distinct physical and chemical properties. Furthermore oxyHb-containing proinflammatory HDL potently consumed nitric oxide and contracted arterial vessels ex vivo. Moreover Hb also was found differentially associated with HDL from coronary heart disease patients compared with healthy controls. Our data suggest that Hb contributes to the proinflammatory nature of HDL in mouse and human models of atherosclerosis and may serve as a novel biomarker for atherosclerosis.

On the use of s-t-butylsulphenyl group for protection of cysteine in solid-phase peptide synthesis using fmoc-amino acids

Abstract The utilization of the N α -fluorenylmethoxycarbonyl derivative of S- t -butyl sulphenyl cysteine in solid-phase peptide synthesis for the preparation of several cysteine-containing peptides is described. When this derivative is located in the C-terminal position a side reaction prevents the formation of the desired product. Finally, a peptide containing a disulphide bond has been obtained in excellent yields by selective deprotection of the cysteines and disulfide bond formation on the solid support.

Method for screening peptide fragment ion mass spectra prior to database searching

A methodology is described for screening fragment ion spectra of peptides prior to database searching for protein identification. A software routine written in the Perl programming language was used to analyze data from previous Sequest database searches and develop a set of statistical descriptors that could be used to identify spectra not likely to yield useful results in a database search. A second Perl program used an evolutionary algorithm to optimize the criteria for each statistical descriptor and generate a formula for determining spectral quality. This formula was used by a third Perl program to screen data sets from four independent liquid chromatography tandem mass spectrometry runs. On the average, use of the screening program reduced the time required for a database search by 1/2 with little loss of useful information from the database search results.

Enzymatic and chemical digestion of proteins for mass spectrometry

Publisher Summary This chapter discusses enzymatic and chemical digestion of proteins for mass spectrometry. The standard approach for obtaining partial or complete structures of proteins without resorting to cloning cDNAs is to digest the purified protein with one or two selected endoproteases or by chemical cleavage methods, then to fractionate the resulting peptides by reversed-phase high-performance liquid chromatography (HPLC), and to sequence the resulting peptides. In the past, peptides have been primarily sequenced by automated Edman chemistry, which currently has a sensitivity in the mid to low picomole range. Wherever possible, structures were confirmed by amino acid compositional analysis which revealed the amount of sample present and the relative molar ratios of each amino acid. With the advent of mass spectrometric techniques such as fast atom bombardment mass spectrometry (FAB-MS), it has been possible to obtain molecular weights for the majority of peptides analyzed, even at the low picomole range. With these objectives in mind, the chapter presents methods for obtaining peptide maps at the 100 pmol level on widely available standard proteins (horse cytochrome c and myoglobin).