Improved resolution in the detection of oligonucleotides up to 60-mers in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using pulsed-delayed extraction with a simple high voltage transistor switch

Zhu, Yiheng; He, Longhui; Srinivasan, Jannavi; Lubman, David M.

doi:10.1002/(sici)1097-0231(19970615)11:9<987::aid-rcm949>3.0.co;2-j

Cited by 26 publications

(21 citation statements)

References 21 publications

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“…Using reflectron TOF, higher mass resolution can be obtained, i.e. 5000–7500,56–62 and mass accuracies for DNA analysis of 30 ppm have been reported 59, 60. It should be emphasized, however, that these measurements are limited to small oligonucleotides (<30mer), and the calibrations are performed with external standards.…”

Section: Introductionmentioning

confidence: 99%

Accurate mass measurement of DNA oligonucleotide ions using high‐resolution time‐of‐flight mass spectrometry

Koomen¹,

Russell²,

Tichy³

et al. 2002

J. Mass Spectrom.

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Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.

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Section: Introductionmentioning

confidence: 99%

Accurate mass measurement of DNA oligonucleotide ions using high‐resolution time‐of‐flight mass spectrometry

Koomen¹,

Russell²,

Tichy³

et al. 2002

J. Mass Spectrom.

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“…The application of IR lasers has extended the limits of detection even further and restriction fragments of plasmid DNA and RNA transcripts up to a size of 2180 nucleotides have been reported 5. However, due to a serious decline in resolution6 and sensitivity7 of MALDI‐TOFMS with an increase in DNA length, the practicality of DNA analysis tends to be limited to lengths up to 50 nucleotides.…”

mentioning

confidence: 99%

Application of DNA‐binding polymers for preparation of DNA for analysis by matrix‐assisted laser desorption/ionization mass spectrometry

Smirnov¹,

Hall²,

Ross³

et al. 2001

Rapid Comm Mass Spectrometry

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The susceptibility of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to the presence of salts in a sample, especially salts of alkali metals, requires careful and often tedious desalting procedures which complicate and slow the throughput of MS-based methods. A novel approach to sample preparation was developed based on the extraction of DNA out of solution onto a solid surface with an attached DNA-binding polymer, such as polyethyleneimine or polyvinylpyrrolidone. The observed binding is strong enough to sustain washing, and, as a result, desalting and concentration can be performed in a single fast step. After DNA has been immobilized on the surface and supernatant solution removed, subsequent addition of MALDI matrix releases material from the surface, which co-crystallizes with matrix. The mass spectrometric analysis is then performed directly from this support. Analysis of oligonucleotides and three-fold multiplexed SNP typing reactions performed by this method shows improved sensitivity and excellent resolution for various DNA fragments, together with high tolerance to various buffer components, such as alkali metals and surfactants. Simplicity and speed make it attractive for high-throughput sample preparation and analysis of oligonucleotide mixtures by MALDI-MS.

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“…C → G) 18,. 20 Furthermore, the formation of adducts can limit mass resolution and sensitivity since it spreads the signal over several mass units 8. It has been observed using a quadrupole ion‐trap mass spectrometer (LCQ, Thermo‐Finnigan, San Jose, CA, USA) that on‐line heating of the sample syringe is required to denature the ds DNA and remove residual adducts 5.…”

Section: Resultsmentioning

confidence: 99%

“…However, generally the size of the PCR products have been minimized because resolution decreases rapidly as the size increases. Indeed, above 65 mers, the resolution is below 100 8. Additionally, the two strands of double‐stranded (ds) PCR products are not generally resolved on MALDI‐TOFMS analysis 9,.…”

mentioning

confidence: 99%

Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometry

Walters

Muhammad

Fox

et al. 2001

Rapid Comm Mass Spectrometry

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Both single nucleotide polymorphisms (SNPs) and mutations are commonly observed in the gene encoding the tumor suppressor protein, p53. SNPs occur at specific locations within genes whereas mutations may be distributed across large regions of genes. When determining nucleotide differences, mass spectrometry is the only method other than Sanger sequencing which offers direct structural information. Electrospray ionization (ESI) quadrupole mass spectrometry (MS) analysis of intact polymerase chain reaction (PCR) products was performed following a simple purification and on-line heating to limit ion adduction. The PCR products were amplified directly from genomic DNA rather than plasmids, as in our previous work. Two known polymorphisms of the p53 gene were genotyped. A cytosine (C) or guanine (G) transversion, designated C <--> G (G <--> C on the opposite strand), were each detected by a 40.0 Da change upon ESI quadrupole MS analysis. Using known PCR products as standards, the genotypes determined for 10 human samples corresponded with restriction fragment length polymorphism (RFLP) analysis. Cytosine/thymine (T) transitions, designated C <--> T (G <--> A on the opposite strand), were also genotyped by ESI-MS. This SNP is discriminated by a 15.0 Da change on one strand (C <--> T) and a 16.0 Da change on the other (G <--> A). Appropriate sample preparation and instrumental configuration (including heated sample inlet syringe and MS source), to limit adducts, are both vital for successful ESI quadrupole MS analysis of intact PCR products.

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Improved resolution in the detection of oligonucleotides up to 60-mers in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using pulsed-delayed extraction with a simple high voltage transistor switch

Cited by 26 publications

References 21 publications

Accurate mass measurement of DNA oligonucleotide ions using high‐resolution time‐of‐flight mass spectrometry

Accurate mass measurement of DNA oligonucleotide ions using high‐resolution time‐of‐flight mass spectrometry

Application of DNA‐binding polymers for preparation of DNA for analysis by matrix‐assisted laser desorption/ionization mass spectrometry

Genotyping single nucleotide polymorphisms using intact polymerase chain reaction products by electrospray quadrupole mass spectrometry

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