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D M Lubman

Publications and source records attributed to D M Lubman.

At least 55 records · Page 3Linked to original sources
PubMed1996

Characterization of two new matrices for matrix-assisted laser desorption/ionization mass spectrometry.

Three structurally related compounds, 4-hydroxy-33-methoxyphenylpyruvic acid (HMPPA), indole-3 pyruvic acid (IPA), and indole-3-glyoxylic acid have been evaluated as matrix-assisted laser desorption/ionization (MALDI) matrices. HMPPA and IPA were found to be effective matrices for MALDI-MS analysis of proteins and peptides and have been characterized in this work. HMPPA was found to be a particularly good matrix for the analysis of proteins and peptides because of its tolerance towards impurities and the resulting sensitivity in MALDI-MS experiments. Analysis of model proteins and peptides, including those in biological fluid, are demonstrated.

Glyoxylates↗
PubMed1996

Capillary liquid chromatography coupled with an ion trap storage/reflectron time-of-flight mass spectrometer for structural confirmation of three recombinant protein isoforms.

Packed-capillary high-performance liquid chromatography (HPLC) was successfully coupled with an ion trap storage/reflectron time-of-flight mass spectrometer (LC/IT/reTOFMS) through an electrospray ionization interface for protein structural elucidation. Using the total-ion storage capabilities of the trap over a broad mass range and the high sensitivity from the packed capillary column with i.d. as small as 250 microns, high sensitivity peptide mapping in the low picomole range was demonstrated for the structural confirmation of three recombinant human nucleoside diphosphate kinase isoforms (NDPK, E.C. 2.7.4.6). A strategy combining chemical/enzymatic digestions as well as collisionally-induced dissociation (CID) in the electrospray source was successfully employed to infer the minor primary structural differences among the three recombinant proteins. This high sensitivity was achieved while also maintaining a resolution of nearly 1500 for mass identification using the capabilities of the IT/reTOF device. A point mutation of serine 120 to glycine was verified between the wild-type NDPK A and its mutant (delta m = 30 u) by both selected-ion monitoring and ion-source CID of the protein fragment containing the mutation site. For the structural confirmation of the sequence of NDPK A and B (88% homology), two sets of chemical/proteolytic digests were generated independently and followed by LC/MS analysis of the molecular weight of each protein-generated fragment. The complementary information from the two chromatographic analyses allowed for sequence verification of the two protein isoforms. The experiments clearly demonstrated that the high concentration sensitivity of the capillary high-performance liquid chromatographic separation together with the advantages of the IT/reTOF mass spectrometer could provide a low-cost, high-performance facility for protein analysis.

Amino Acid Sequence↗
PubMed1996

The development of a data system for a combination of liquid chromatography or capillary electrophoresis with an ion trap storage/reflectron time-of-flight mass detector.

A data system based upon a 200 MHz transient recorder interface card in a Pentium PC computer is demonstrated for on-line analysis of microbore high-performance liquid chromatography (HPLC), capillary HPLC and capillary electrophoresis (CE) separations using a fast and sensitive ion-trap storage/reflectron time-of-flight mass spectrometric detector (IT-reTOFMS). Under the control of a user-written program, the system is capable of conducting the data acquisition and storage for a minimum of 30 min, at rates exceeding 10 Hz, of individual mass spectra containing 16,000 data points having 10 nsec resolution. The capability is mainly attributed to the use of a data reduction scheme in which only mass intensities higher than a preset threshold are saved as indexed flight-time/intensity pairs. This produces a typical reduction ratio of 30:1 in data set size, yielding faster storage with smaller file size, and permits the complete set of mass spectra to be held in the computer's memory. In addition, the data system is capable of displaying, for real-time evaluation of the analysis, each individual mass spectrum and the total-ion chromatogram. Further, the selected-ion chromatograms of given masses and a 3-dimensional topographic map describing a separation process can be rapidly generated from the collected data for the unambiguous and high fidelity identification of target analytes in a complex mixture.

Amino Acid Sequence↗
PubMed1996

Determination of bacterial protein profiles by matrix-assisted laser desorption/ionization mass spectrometry with high-performance liquid chromatography.

A rapid method for profiling bacterial and cellular proteins has been developed using a combination of capillary high-performance liquid chromatography separation followed by (MALDI-MS) matrix-assisted laser desorption/ionization mass spectrometric analysis. In this method, bacteria are sonicated, the cell walls broken, and the water-soluble proteins precipitated for analysis. The proteins are separated by capillary liquid chromatography and detected on-line by a UV absorption detector. The eluents are then collected for off-line analysis by MALDI-MS. Using this method, it is demonstrated that bacteria can be discriminated based upon their protein profiles to the species level with only pmol level detection of proteins. It has also proved to be a fast and accurate means for monitoring the expression of Hsp27 in an insect cell system.

Animals↗
PubMed1996

Procedures for tandem mass spectrometry on an ion trap storage/reflectron time-of-flight mass spectrometer.

In this work, we demonstrate tandem mass spectrometry on an ion trap storage-reflectron time-of-flight mass spectrometer (IT/reTOFMS). Ion isolation and activation were achieved by resonant excitation using multi- and single-frequency waveforms generated from an analog circuit. Product-ion spectra of small polypeptides are obtained, which are comparable in fragmentation to those acquired on sector or hybrid mass spectrometers. Several important parameters governing the tandem mass spectrometry process, including the activation tickle voltage, type of collision gas, activation period and cooling period after the fragmentation were optimized using leucine-enkephalin as a model. Although the limited energy deposition from collisional activation in our experiments does not allow efficient fragmentation of large singly charged polypeptides with m/z higher than 1000, the problem may be partially solved by taking advantage of fragmenting the multiply charged ions produced from the electrospray ionization source as demonstrated for a synthetic polypeptide of molecular weight 2782. Compared to the singly charged form, the reduced m/z of multiply charged forms experience a greater trapping force as described by the pseudopotential well-depth model. Increased pseudopotential well-depths for multiply charged species permit the use of greater fragmentation energy at lower RF potentials. These conditions facilitate the fragmentation of large polypeptides, yet are suitable for trapping singly charged fragments. These experiments indicate that the high efficiency associated with ion dissociation and fragment-ion collection in the trap and the storage capability for detection of ions using the non-scanning mode of the IT/ reTOF analyzer may provide an alternative means for acquiring sequence-specific information of polypeptides at low picomol levels of sensitivity.

Amino Acid Sequence↗
PubMed1995

Use of a nitrocellulose film substrate in matrix-assisted laser desorption/ionization mass spectrometry for DNA mapping and screening.

A nitrocellulose film is used as a substrate in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) studies of DNA. PCR products and DNA fragment digests obtained from biochemical procedures can be analyzed with the use of a nitrocellulose substrate in MALDI MS whereas no signal is observed with the use of a stainless steel substrate. In this method, on-probe purification allows for effective elimination of the interfering effects of salts, buffers, and other contaminants that are usually present in DNA samples, which serve as important limiting factors in the DNA molecular ion yield in the MALDI process. The use of the nitrocellulose film substrate also appears to improve the shot-to-shot and sample-to-sample reproducibility of the ion yield due to the more homogeneous coverage of matrix/analyte over the sample surface. With the use of the nitrocellulose substrate, DNA fragments of up to 622 base pairs in complex mixtures provide mass spectra with minimal sample purification. Although only species corresponding to single-stranded DNA were detected, a mass calibration scheme was established allowing an accuracy of within one base pair for fragments of < 250 bp under the experimental conditions. Despite the low mass resolution of the spectra obtained, the method has been successfully used for rapid DNA screening for sample disease genes and PCR products.

Base Sequence↗
PubMed1995

Analysis of tryptic digests using microbore HPLC with an ion trap storage/reflectron time-of-flight detector.

An electrospray ionization source interfaced to an ion trap storage/reflectron time-of-flight mass spectrometer is evaluated as a rapid, sensitive detector for microbore HPLC. Using the total ion storage capabilities of the trap over a broad mass range, total ion chromatograms of tryptic digests of bovine cytochrome c and bovine beta-casein are obtained following microbore HPLC separations with samples in the low picomole range. The digests are analyzed with the aid of software developed in our laboratory, which can display the selected ion chromatogram (SIC) for each chromatographic peak. The SIC mode can be used for enhancement of the S/N and for identification of a chromatographic peak with a particular mass. In addition, the mass spectrum corresponding to each chromatographic peak can be displayed to check for unresolved chromatographic components.

Amino Acid Sequence↗
PubMed1995

Sequence-specific fragmentation generated by matrix-assisted laser desorption/ionization in a quadrupole ion trap/reflectron time-of-flight device.

Sequence-specific fragmentation for structural analysis has been generated by activation of ions via matrix-assisted laser desorption/ionization (MALDI) in an ion trap storage/reflectron time-of-flight device (IT/reTOF). The key to this work is that ion decay can be induced by MALDI activation but requires an extended period of time to occur in large peptides. This extended decay period, which may be in excess of 20 ms, is provided in these experiments using the long storage times of the ion trap device. The ions are stored until decay is complete and then rapidly pulsed into a reflectron TOF for analysis. Since the ions decay within the trap, they ultimately appear as stable ions in the reTOF rather than as metastable decay peaks. The ion fragmentation was found to depend strongly on laser power and the rf voltage placed on the ring electrode of the trap. The fragmentation obtained was shown to be similar to but different from that observed in FAB-low-energy CAD. In particular, enhanced fragmentation was obtained in the lower mass range and large species could be more easily fragmented than with FAB-low-energy CAD. The types of fragmentation for several target peptides are discussed.

Amino Acid Sequence↗
PubMed1995

Rapid screening of genetic polymorphisms using buccal cell DNA with detection by matrix-assisted laser desorption/ionization mass spectrometry.

A new approach is developed for the rapid and cost-effective detection of human genetic polymorphisms based on matrix-assisted laser description/ionization mass spectrometric (MALDI MS) detection using a nitrocellulose film substrate. This method employs polymerase chain reaction (PCR) amplification using DNA extracted from buccal cells as templates, followed by direct digestion with restriction enzymes and subsequent analysis by MALDI MS. The extraction of DNA from buccal cells provides a rapid and convenient means for sampling PCR-based diagnostic analysis. The amount of DNA was sufficient as the template for both normal PCR amplifications, and amplifications involving the use of mismatched primers and multiple primers. The MALDI MS methodology has been successfully used for the analysis of such PCR products where restriction fragments generated directly in PCR reactions have been used for detection of carbonic anhydrase and cystic fibrosis transmembrane conductance regulator as model genes. The detection of genetic polymorphisms following routine biological and clinical procedures with the MALDI MS method is demonstrated. The results from MALDI MS analysis are shown to be comparable to those obtained from gel electrophoresis but the MALDI MS method is several orders of magnitude faster than gel electrophoretic techniques. The method described herein should also be readily extended to other areas involving DNA screening and testing.

Base Sequence↗
PubMed1995

Collision-induced dissociation of multiply charged peptides in an ion-trap storage/reflectron time-of-flight mass spectrometer.

Single-frequency collisional activation of multiply charged peptides has been studied via electrospray ionization in an ion trap storage/reflectron time-of-flight device (IT/reTOF). Several peptides with molecular weights ranging from 600 to 1700 were used to demonstrate that sequence information can be obtained with this hybrid instrument with a sensitivity in the low picomole level. Further, a resolution of nearly 1000 can be obtained for the fragment products, due to the cooling effects of the buffer gas in the trap before analysis by the reTOF. The influence of the primary structure of the peptides on the observed collision-induced fragmentation patterns is discussed. Although the current study is limited by the electronics, in terms of its ion isolation capabilities, it is demonstrated that the device has the potential for obtaining sequence information for peptides with excellent sensitivity and relatively high resolution.

Amino Acid Sequence↗
PubMed1994

Matrix-assisted laser desorption/ionization using an active perfluorosulfonated ionomer film substrate.

The use of an active Nafion substrate is shown to enhance the performance of MALDI MS. The use of a Nafion substrate with certain matrices can significantly enhance the signals obtained over those observed with a stainless steel probe substrate. Analytes can often be observed with the use of the Nafion substrate that cannot be easily observed with the standard MALDI procedure, and usually a much wider range of peaks can be observed using MALDI from the Nafion substrate than with any single matrix on a stainless steel substrate. This enhancement of signal from the Nafion substrate is observed only with the sequential deposition of the sample and the matrix onto the Nafion film. If the analyte and matrix are premixed, then the effect is not observed. The use of the Nafion substrate has been shown to be particularly effective in analyzing real biological mixtures without prepurification. This has been demonstrated for various samples including the analysis of the products of chemical digests of proteins, protein profiling in milk and egg white samples, cell lysate analysis, and oligonucleotide detection.

Fluorocarbon Polymers↗
PubMed1994

Ion fragmentation activated by matrix-assisted laser desorption/ionization in an ion-trap/reflectron time-of-flight device.

An ion-trap storage/reflectron time-of-flight mass spectrometer has been used to study the decay of large ions following activation by matrix-assisted laser desorption/ionization (MALDI). It is shown that large ions may undergo fragmentation over long periods of time, extending even to milliseconds in some cases. These fragments are stored in the trap and detected as stable ions in the reflectron device, rather than as metastable ions due to decay during the flight time to the detector. The ion decay is found to depend strongly on the laser intensity, while a smaller effect may be due to the matrix used in the MALDI process. The fragmentation observed was found to also depend strongly on the RF voltage applied to the ring electrode; higher RF voltage produced enhanced fragmentation. A gated RF experiment further demonstrated the importance of the level of the RF voltage, during the initial activation event, in producing fragmentation. A study of the effects of buffer gas composition and pressure showed that increased pressure may result in reduced fragmentation due to collisional cooling in the trap. However, the use of argon or nitrogen buffer gas at increased pressure in the trap may result in fragmentation upon extraction from the trap, producing metastable ions in the flight tube. The implications of the use of the time variable for obtaining fragmentation in the trap for rapid sequencing are discussed.

Amino Acid Sequence↗
PubMed1994

Matrix-assisted laser desorption/ionization mass spectrometry of restriction enzyme-digested plasmid DNA using an active Nafion substrate.

Matrix-assisted laser desorption/ionization using a 3-hydroxypicolinic acid matrix from an active Nafion substrate has been used for detection of restriction enzyme-digested double-stranded plasmid DNA using time-of-flight mass spectrometry. DNA strands of up to 267 base pairs were detected with minimal sample purification, although only as species corresponding to single-stranded DNA.

Base Sequence↗
PubMed1993

Phorbol 12-myristate 13-acetate-induced phosphorylation of Op18 in Jurkat T cells. Identification of phosphorylation sites by matrix-assisted laser desorption ionization mass spectrometry.

Op18 is a widely expressed, cell cycle-regulated, phosphoprotein involved in signal transduction of a variety of stimuli. In actively proliferating Jurkat T cells which express Op18 at high level, phorbol 12-myristate 13-acetate (PMA) treatment induces a rapid increase in the level of several Op18 phosphorylated forms. To determine phosphorylation sites involved in the PMA effect, the major Op18 phosphorylated forms were resolved in Jurkat T cells, before and after treatment with PMA, using preparative immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis. Tryptic fragments of phosphorylated Op18 were analyzed by two-dimensional thin layer peptide mapping and were resolved by reverse-phase high performance liquid chromatography prior to analysis by matrix-assisted laser desorption ionization mass spectrometry. Phosphorylation sites were identified by further treatment of the proteolytic fragments with different enzymes and determination of the mass shifts by matrix-assisted laser desorption ionization mass spectrometry. Two major phosphorylation sites were identified. Low constitutive levels of phosphorylation at Ser25 and Ser38 in Op18a and Op18b was demonstrated. Treatment with PMA resulted in enhanced phosphorylation of Ser25 in Op18a and of both Ser25 and Ser38 in Op18b. Taken together with prior studies of Op18 phosphorylation, the data suggest that Op18 phosphorylation occurs at identical sites in different tissues and organisms.

Amino Acid Sequence↗
PubMed1993

Detection of liquid injection using an atmospheric pressure ionization radiofrequency plasma source.

An atmospheric pressure rf plasma source which operates in a variety of different buffer gases has been developed as an ionization method for organic samples introduced by liquid injection into atmospheric pressure ionization mass spectrometry (API/MS). The rf source can operate in He at < 1 W of load power at 165 kHz. It can also be sustained in Ar, N2, air, and CO2 at a load power of < 15 W. In most cases studied, the protonated molecule, MH+, is observed with little or no fragmentation even under the relatively high current conditions of the discharge. However, using increasingly higher acceleration voltages between the skimmers in the differentially pumped region between atmospheric pressure and high vacuum, one can induce fragmentation via collision-induced dissociation. This can be assisted in these experiments via the use of a heavy buffer gas. The detection limits achieved for rf/API plasma detection are typically in the low femtomole region for small organic molecules including neurotransmitters, PTH-amino acids, steroids, drugs, pesticides, and explosives. The detection can be performed with quantitation over at least 4 orders of magnitude.

Air Ionization↗
PubMed1992

Liquid sample injection using an atmospheric pressure direct current glow discharge ionization source.

An atmospheric pressure DC glow discharge in helium has been used as an ionization source for organic samples introduced by liquid injection into atmospheric pressure ionization mass spectrometry (API/MS). The glow source operates typically in the range up to 1 mA of current at less than 1 kV, although the source can be operated up to a discharge current of 10 mA. Even at the high current used in this work, the protonated molecule, MH+, is observed with little or no fragmentation for many of the samples studied. The detection limits achieved for API glow discharge detection are typically in the low femtomole region for small organic molecules including small biological neurotransmitters, drugs, pesticides, phenylthiohydantoin-substituted amino acids, and explosives. A detection limit of approximately 2 pg has been achieved for tyramine with linear quantitation over at least 3 orders of magnitude. The sensitivity in these experiments has been further improved by optimization of the skimmer-interface system and the liquid injection/nebulization design.

Amino Acid Sequence↗