Exploring the Versatility of Micro-flow Technology – From Peptide Biomarkers ...Waters Corporation
Presenter: Corey D. Broeckling, Ph.D., Associate Director, Proteomics and Metabolomics Facility, Joint Assistant Professor, Colorado State University
Microfluidic technology offers multiple advantages including ease of use, robustness and sensitivity. Coupled with a tandem quadrupole mass spectrometer (such as the Xevo TQ-S) we can create an optimal and versatile “middle ground” platform in which these advantages can be exploited for both small molecule and peptide quantitative applications. For example, most small molecule applications are performed using standard flow chromatography (in the range of 600-100 L/min) consuming a high level of both solvent and sample which increases the cost (both fiscally and environmentally). The use of microfluidic technology for these small molecule applications can reduce solvent consumption by upwards of 150-fold and can significantly increase on-column sensitivity, thus reducing sample consumption. Conversely, quantitative peptide assays are almost exclusively performed using nanoscale chromatography (~400 nL/min) to achieve the required sensitivity for detection of these low abundance molecules within a complex matrix (e.g. serum, urine, etc.). We have found that the use of microfluidic technology for peptide quantitation yields the same or better sensitivity when compared to a nanoscale platform and has the additional, very significant advantages of ease of use, robustness, and improved chromatographic resolution (e.g. peak capacity). Thus, with a single analytical platform we can perform quantitative analysis for a wide range of compounds spanning from lipids/metabolites to peptides. One application in which the technology has struggled is the analysis of compounds in negative ionization mode. This limitation has been overcome in the development of a next generation microfluidic device that incorporates post-column addition of isopropanol to improve ionization and spray stability in negative mode applications. With this new capability we can now perform quantitative experiments in negative mode or with polarity switching.
This presentation was given at the 11th International Conference of the Metabolomics Society (Metabolomics 2015, #metsoc2015 on Twitter), June 29, 2015, in San Francisco.
Exploring the Versatility of Micro-flow Technology – From Peptide Biomarkers ...Waters Corporation
Presenter: Corey D. Broeckling, Ph.D., Associate Director, Proteomics and Metabolomics Facility, Joint Assistant Professor, Colorado State University
Microfluidic technology offers multiple advantages including ease of use, robustness and sensitivity. Coupled with a tandem quadrupole mass spectrometer (such as the Xevo TQ-S) we can create an optimal and versatile “middle ground” platform in which these advantages can be exploited for both small molecule and peptide quantitative applications. For example, most small molecule applications are performed using standard flow chromatography (in the range of 600-100 L/min) consuming a high level of both solvent and sample which increases the cost (both fiscally and environmentally). The use of microfluidic technology for these small molecule applications can reduce solvent consumption by upwards of 150-fold and can significantly increase on-column sensitivity, thus reducing sample consumption. Conversely, quantitative peptide assays are almost exclusively performed using nanoscale chromatography (~400 nL/min) to achieve the required sensitivity for detection of these low abundance molecules within a complex matrix (e.g. serum, urine, etc.). We have found that the use of microfluidic technology for peptide quantitation yields the same or better sensitivity when compared to a nanoscale platform and has the additional, very significant advantages of ease of use, robustness, and improved chromatographic resolution (e.g. peak capacity). Thus, with a single analytical platform we can perform quantitative analysis for a wide range of compounds spanning from lipids/metabolites to peptides. One application in which the technology has struggled is the analysis of compounds in negative ionization mode. This limitation has been overcome in the development of a next generation microfluidic device that incorporates post-column addition of isopropanol to improve ionization and spray stability in negative mode applications. With this new capability we can now perform quantitative experiments in negative mode or with polarity switching.
This presentation was given at the 11th International Conference of the Metabolomics Society (Metabolomics 2015, #metsoc2015 on Twitter), June 29, 2015, in San Francisco.
Metabolomics & Lipidomics: From Discovery to Routine ApplicationsWaters Corporation
Presenter: Giuseppe Astarita, Ph.D., Principal Scientist, Waters Corp, Adjunct Professor, Georgetown University
A number of technological advancements have enhanced our ability to conduct metabolomics and lipidomics experiments. State-of-the-art chromatography, ionization sources, and MS technology combined with powerful informatics solutions provide a comprehensive set of tools to analyze complex mixtures of lipids and polar metabolites in biological samples. In this presentation, I will illustrate current workflows for metabolomics & lipidomics, including untargeted and targeted approaches, for discovery and routine applications.
This presentation was given at the 11th International Conference of the Metabolomics Society (Metabolomics 2015, #metsoc2015 on Twitter), June 29, 2015, in San Francisco.
Abstract
A small set of amphetamines has been analyzed by gas chromatography (GC) high-resolution time-of-flight mass spectrometry (TOFMS) using a microplasma photoionization (MPPI) soft-ionization source. This plasma-based, wavelength selectable ionization source enables ionization of the test compounds and their corresponding derivatives at ~8-12 eV that is a softer alternative to electron ionization at 70 eV. Three plasma gases were used in this study: Xe plasma that emits photons at resonance lines of 9.57 eV and 8.44 eV; Kr plasma at 10.63 eV and 10.02 eV, and Ar plasma at 11.82 eV and 11.61 eV. Derivatization of the test compounds with trifluoroacetic anhydride and α-methoxy-α-(trifluoromethyl)-phenylacetyl pyrazole was evaluated because the MPPI mass spectra of the underivatized amphetamines yield primarily iminium ions, which make the identification of the test compounds by GC-TOFMS inconclusive. The MPPI mass spectra of the TFA-derivatized amphetamines yield abundant molecular ions, when using Xe as plasma gas, and enough fragment ions with the Ar plasma that can help in formula generation. The structure elucidation of two "known unknowns" designer drugs using this "tunable" soft-ionization source and a high-resolution TOF mass spectrometer is presented in this study.
Metabolomics & Lipidomics: From Discovery to Routine ApplicationsWaters Corporation
Presenter: Giuseppe Astarita, Ph.D., Principal Scientist, Waters Corp, Adjunct Professor, Georgetown University
A number of technological advancements have enhanced our ability to conduct metabolomics and lipidomics experiments. State-of-the-art chromatography, ionization sources, and MS technology combined with powerful informatics solutions provide a comprehensive set of tools to analyze complex mixtures of lipids and polar metabolites in biological samples. In this presentation, I will illustrate current workflows for metabolomics & lipidomics, including untargeted and targeted approaches, for discovery and routine applications.
This presentation was given at the 11th International Conference of the Metabolomics Society (Metabolomics 2015, #metsoc2015 on Twitter), June 29, 2015, in San Francisco.
Abstract
A small set of amphetamines has been analyzed by gas chromatography (GC) high-resolution time-of-flight mass spectrometry (TOFMS) using a microplasma photoionization (MPPI) soft-ionization source. This plasma-based, wavelength selectable ionization source enables ionization of the test compounds and their corresponding derivatives at ~8-12 eV that is a softer alternative to electron ionization at 70 eV. Three plasma gases were used in this study: Xe plasma that emits photons at resonance lines of 9.57 eV and 8.44 eV; Kr plasma at 10.63 eV and 10.02 eV, and Ar plasma at 11.82 eV and 11.61 eV. Derivatization of the test compounds with trifluoroacetic anhydride and α-methoxy-α-(trifluoromethyl)-phenylacetyl pyrazole was evaluated because the MPPI mass spectra of the underivatized amphetamines yield primarily iminium ions, which make the identification of the test compounds by GC-TOFMS inconclusive. The MPPI mass spectra of the TFA-derivatized amphetamines yield abundant molecular ions, when using Xe as plasma gas, and enough fragment ions with the Ar plasma that can help in formula generation. The structure elucidation of two "known unknowns" designer drugs using this "tunable" soft-ionization source and a high-resolution TOF mass spectrometer is presented in this study.
Identification and characterization of intact proteins in complex mixturesExpedeon
The ability to fully characterize proteins in their intact forms allows thorough biological investigation of the functional importance of changes such as post-translational modifications, protein isoforms/sequence variations, and protease cleavages.
Analysis of tomato metabolite variations via liquid chromatography mass spect...Arthur Stem
Numerous factors can influence metabolite profiles of tomato variants and the fruits they produce. The focus of this project is a comparative metabolomic analysis of the high pigment-2dg (hp-2dg) tomato mutant with its wild type counterpart (‘Manapal’) at early and late developmental stages. The goal is to determine if differences can be found using an “untargeted” metabolomics approach.
Stability Indicating RP HPLC Method Development and Validation of Everolimus ...ijtsrd
Everolimus is semisynthetic derivative of sirolimus, which is isolated from Streptomyces hygroscopicus. A novel reversed phase high performnce liquid chromatography HPLC method for determination of the everolimus in the presence of degradation product or pharmaceutical excipients. Seperation was carried out using Cosmosil C18 250mm x 4. 6ID , column having particle size 5 micron using acetonitrile and methanol mixture, and pH adjusted to 3, a flow rate of 1. 0 mL min, and ultraviolet detection at 285nm. A retention time nearly 3. 806 min was observed. The calibration curve for everolimus was linear from range of 5 25 µg mL with limit of detection and limit of quantitation of 0. 0817 and 0. 2478 µg mL, respectively. Analytical validation parameters such as selectivity, specificity, linearity, accuracy and precision were evaluated and relative standard deviation value for all the key parameters were less than 2. 0 . The stability indicating method was developed by exposing the drug to stress conditions of acid and base hydrolysis, oxidation, photodegradation, and thermal degradation the obtained degraded products were successfully seperated from the APIs. This method was validated in acceptance with ICH guidelines and results within the acceptance criteria. Rushikesh Mulay | Rishikesh Bachhav "Stability Indicating RP-HPLC Method Development and Validation of Everolimus in Bulk and Pharmaceutical Dosage Form" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-5 | Issue-6 , October 2021, URL: https://www.ijtsrd.com/papers/ijtsrd46341.pdf Paper URL : https://www.ijtsrd.com/pharmacy/analytical-chemistry/46341/stability-indicating-rphplc-method-development-and-validation-of-everolimus-in-bulk-and-pharmaceutical-dosage-form/rushikesh-mulay
A next generation sequencing based sample-to-result pharmacogenomics research...Thermo Fisher Scientific
Pharmacogenomics (PGx) is the study of genetic variations in terms of their response to drugs. Variations in gene sequence or copy numbers may result in complete loss of function, partial decrease or increase in enzyme activity, or an altered affinity for substrates, which may in turn significantly impact drug efficacy. PGx studies are becoming increasingly important for precision medicine. We have developed a next generation sequencing (NGS) PGx research solution with increased flexibility on the assay targets and combined detection of SNP/INDEL genotyping and CNV using Ion AmpliSeq™ technology for low to medium throughput laboratories. With this highly multiplexed PGx research panel we can profile a set of 136 genetic markers in 40 known PGx related genes (Table 1) and determine CYP2D6 copy number variation (CNV, Figure 1) in a single reaction using Ion Torrent™ semiconductor sequencing.
Next generation sequencing of the whole transcriptome enables high resolution measurement of gene expression activity in different tissue and cell types. This methodology provides an in depth study of known transcripts and depending on the data analysis, allows identification of additional transcript types such as transcript variants, fusion transcripts, and small and long ncRNAs.
In this study we performed RNA-Seq using the Ion Torrent™ sequencing platform to compare the expression profile of testicular germ cell cancers (seminoma type, n=3) and normal testis (n=3). Using Partek Flow® 3.0 and TopHat/BowTie or Star aligners, we aligned the reads to the human genome and mapped sequences to the RefSeq database. Differentially expressed genes were identified and screened with additional germ cell tumors.
PCA analysis showed clear separation of the two sample types indicating biological differences. List of differentially expressed genes generated from TopHat/Bowtie and Star were similar. We identified a large number of genes that were up and down regulated with high degree of significance (p<0.01,>2X FC (fold change)). These included genes related to testicular tissue type, stem cell pluripotency (NANOG; POU5F1) and proliferation (KRAS, CCND2).
In addition, a number of differentially expressed noncoding RNAs were identified (SNORD12B, XIST). The method was validated on a small set of genes (n=20) using qPCR (TaqMan® Assays) and were found to be correlated. We used the OpenArray® platform to quickly and quantitatively screen 102 differentially expressed genes and 10 endogenous control genes across a number of different testicular germ cell cancer types.
We used a complete work flow solution from sample prep to NGS to qPCR to compare the expression profile of normal testis and seminoma type germ cell tumors. From the NGS experiments we identified a large number of differentially expressed genes for qPCR screening with samples from different types of germ cell tumors. Results from these screening studies will be presented.
Abstract book for the following conferences:
2013 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS 2013)
2013 2nd International Conference on Environment, Energy and Biotechnology (ICEEB 2013)
2013 2nd International Conference on Chemical and Process Engineering (ICCPE 2013)
2013 2nd Journal Conference on Environmental Science and Development (JCESD 20132nd)
The conferences was held at Concorde Inn Kuala Lumpur International Airport, Malaysia on 09 June 2013
1. GenoMass: Software tool for high-throughput screening of the LC-MS/MS data to identify the exact location of adducts in
modified Oligonucleotides
Vaneet Sharma,1
James Glick,1
Qing Liao,2
and Paul Vouros1
1
Barnett Institute & Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA; 2
Shenitech LLC, Woburn, MA
GenoMass: Software tool for high-throughput screening of the LC-MS/MS data to identify the exact location of adducts in
modified Oligonucleotides
Vaneet Sharma,1
James Glick,1
Qing Liao,2
and Paul Vouros1
1
Barnett Institute & Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA; 2
Shenitech LLC, Woburn, MA
Synthesis & characterization of monolithic poly(styrene divinylbenzene)−
columnsA 10 cm piece of polyimide coated fused silica capillary tubing of 375 μm o.d. and 250 μm i.d. [Polymicro
Technologies, (Phoenix, AZ)] was silanized with 3-(trimethoxysilyl)propyl methacrylate and then filled with a mixture
comprising 50 μL of styrene, 50 μL of divinylbenzene, 135 μL of decanol, 15 μL of tetrahydrofuran, and 10 mg/mL of
azobisisobutyronitrile (AIBN), polymerized at 70 ° C for 24 h. After polymerization capillaries were flushed
extensively with acetonitrile4
.
Unique isomer Mass List in
response to the search performed in
input file
Extracted ion Chromatogram
1477.47
Extracted ion chromatogram
1495.59
Search
Parameters
SampleSeparatio
n
DataAnalysis
Oligonucleotide
Adducts mixture
Ion pair Reversed
Phase
μ-HPLC-negative-ESI-
IT-MS Separation
GenoMass Software
Mass Spectrometry
data
Mobile Phase A: 100% 25mM
triethylammonium bicarbonate (TEAB), pH
8.43
, Mobile Phase B: 100% Methanol,
gradient: 5% to 50% MeOH in 23 min,
mixture of 30 pmol of each modified
oligonucleotide loaded onto the column.
Monolithic
column
μESI
(µL/min
)
PSDVB
0.25X100mm
5-6
GenoMass software is written in visual basic 6.0 under Windows
XP1
.
GenoMass software utilizes client-server architecture for
implementing the ‘reversed pseudo-combinatorial’ approach.
GenoMass is potentially a high-throughput computer software
capable of fast and efficient data mining of complex mass
spectrometric data for nucleic acid analysis.
GenoMass Software automate the data analysis by searching
input data file (LC-MS/MS data) for all possible base sequences
and their modified products.
14 mer 5’-PO4 –ACC CG1C G2TC CG3C G4C-3’OH,
(representing codons 156–159 of p53 gene), Oligonucleotides were
adducted with carcinogenic N-acetoxy-N-acetyl-2-aminofluorene
(AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP) by
previously described methods1,2
.
Unique isomer Mass ListUnique isomer Mass List
Built n-mer isomer mass
table on the fly if n<8 & Built
n-mer isomer mass table in
advance if n >9
Built n-mer isomer mass
table on the fly if n<8 & Built
n-mer isomer mass table in
advance if n >9
Convert raw file to
GenoMass format
Convert raw file to
GenoMass format
Flow charts of
GenoMass software
Flow charts of
GenoMass software
Tandemmassspectrometryinput
W,X,Y,Zseries
a,b,c,d,(a-B)series
SearchParametersSearchParameters
Gene SequenceGene Sequence
Load input fileLoad input file
Multi
charge
search
Run analysisRun analysis
Isomer type
(mer)
Isomer
containing
G/A/C/T
Adduct
search
LC/MS separation of oligonucleotide mixture using
monolithic column with the ion-pairing reagent (TEAB)
conditions
5’OH- TTT TTT TTT TTT TTT T -3’OH
van deemter H-u curve Average Pore size, 160.4 nm,
(Hagen-poiseuille law)
5’OH- TTTTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTT -3’OH
ABP W9
5’-PO4 –ACC CG1 C G2TC CG3C G4C-
3’OH (a5-
B5)
AAAF
5’-PO4 –ACC CG1 CG2TC CG3C G4C-
3’OH (a5-B5)
W9
Input FileInput File
Results & DiscussionOverview
References
5’OH 3’OH
A high throughput screening method for identification of exact location of adducts on modified oligonucleotide ([ds 5’-PO4
-
-ACCCGCGTCCGCGC-3’/5’-GCGCGGGCGCGGGT-3’] modified
with adducts N-acetoxy-N-acetyl-2-aminofluorene (AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP))) is presented. The method is based on the tandem mass spectrometry aspect
of GenoMass software using ion pair reversed phase high performance liquid chromatography (IP-RP- -HPLC) via monolithic poly(styrene divinylbenzene) (PS DVB) capillaryμ μ − −
column coupled to electrospray ionization Ion Trap Mass Spectrometry (ESI-IT-MS).
A high throughput screening method for identification of exact location of adducts on modified oligonucleotide ([ds 5’-PO4
-
-ACCCGCGTCCGCGC-3’/5’-GCGCGGGCGCGGGT-3’] modified
with adducts N-acetoxy-N-acetyl-2-aminofluorene (AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP))) is presented. The method is based on the tandem mass spectrometry aspect
of GenoMass software using ion pair reversed phase high performance liquid chromatography (IP-RP- -HPLC) via monolithic poly(styrene divinylbenzene) (PS DVB) capillaryμ μ − −
column coupled to electrospray ionization Ion Trap Mass Spectrometry (ESI-IT-MS).
1) Liao, Q., Shen, C. and Vouros, P. (2009), GenoMass - a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests.
Journal of Mass Spectrometry, 44: 549–560.
2) Chowdhury, G. and Guengerich, F. (2008), Direct Detection and Mapping of Sites of Base Modification in DNA Fragments by Tandem Mass Spectrometry. Angewandte Chemie
International Edition, 47: 381–384.
3) , Xiong, W., Glick, J,, Lin Y., and, Vouros. P. (2007), Separation and Sequencing of Isomeric Oligonucleotide Adducts Using Monolithic Columns by Ion-Pair Reversed-Phase
Nano-HPLC Coupled to Ion Trap Mass Spectrometry Analytical Chemistry 79 (14), 5312-5321.
4) Premstaller, A., Oberacher, H., Walcher, W., Timperio, A. M., Zolla, L., Chervet, J-P., Cavusoglu, N., Dorsselaer, A. V., and, Huber, C. G., (2001), High-Performance Liquid
Chromatography Electrospray Ionization Mass Spectrometry Using Monolithic Capillary Columns for Proteomic Studies,− Analytical Chemistry 73 (11), 2390-2396 This work was supported by grant from the National Institutes of Health RO169390
W2
-
W3
-
W4
-
W5
-
W6
-
W7
2-
W8
2-
W9
2-
W12
2-
856.65 1145.8
7
1474.7
9
1763.98 1026.58 1178.68 1343.28 1487.88 1941.67
(a13-
B13)2-
(a12-
B12)2-
(a11-
B11)2-
(a10-
B10)2-
(a9-
B9)2-
(a7-
B7)2-
(a6-
B6)-
(a5-B5)-
(a4-B4)-
1903.75 1759.17 1594.58 1449.97 1305.3
8
1977.38 1688.
16
1357.6
5
1069.7
7
W2
-
W3
-
W4
-
W5
-
W6
-
W7
2-
W8
2-
W9
2-
W11
2-
W12
2-
634.42 923.61 1252.79 1541.98 1831.67 1067.69 1232.28 1376.87 1770.58 1915.17
(a11-B11)2-
(a10-B10)2-
(a9-B9)2-
(a7-B7)2-
(a6-B6)-
(a5-B5)-
(a4-B4)-
1678.577 1533.97 1389.37 1072.68 1856.16 1357.73 1069.60
MS/MS
1495.59
MS/MS
1477.47
Load Input File for
(a5-B5)-
(Converted to
GenoMass format)
Conclusions
Load Input File for
W9
2-
(Converted to
GenoMass format)
N-hydroxy-4-aminobiphenyl
(N-OH-4-ABP)
modified 14 mer
N-acetoxy-N-acetyl-2-
aminofluorene (AAAF)
modified 14 mer
GenoMass
Software graphical
user interface
GenoMass
Software graphical
user interface
GenoMass is a unique software which connects tandem mass spectrometry (MS/MS) to a
combinatorial isomer library generated in silico for nucleotide <12 to identify a modified
Oligonucleotide and exact location of adduct.
GenoMass software correctly determines the existence of monoadducted positional isomers for ABP-
oligonucleotide, and AAAF-oligonucleotide.
Genomass software bridges the experimental MS/MS data and human genome database through
sequencing the modified oligonucleotides.
Acknowledgment
![GenoMass: Software tool for high-throughput screening of the LC-MS/MS data to identify the exact location of adducts in
modified Oligonucleotides
Vaneet Sharma,1
James Glick,1
Qing Liao,2
and Paul Vouros1
1
Barnett Institute & Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA; 2
Shenitech LLC, Woburn, MA
GenoMass: Software tool for high-throughput screening of the LC-MS/MS data to identify the exact location of adducts in
modified Oligonucleotides
Vaneet Sharma,1
James Glick,1
Qing Liao,2
and Paul Vouros1
1
Barnett Institute & Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA; 2
Shenitech LLC, Woburn, MA
Synthesis & characterization of monolithic poly(styrene divinylbenzene)−
columnsA 10 cm piece of polyimide coated fused silica capillary tubing of 375 μm o.d. and 250 μm i.d. [Polymicro
Technologies, (Phoenix, AZ)] was silanized with 3-(trimethoxysilyl)propyl methacrylate and then filled with a mixture
comprising 50 μL of styrene, 50 μL of divinylbenzene, 135 μL of decanol, 15 μL of tetrahydrofuran, and 10 mg/mL of
azobisisobutyronitrile (AIBN), polymerized at 70 ° C for 24 h. After polymerization capillaries were flushed
extensively with acetonitrile4
.
Unique isomer Mass List in
response to the search performed in
input file
Extracted ion Chromatogram
1477.47
Extracted ion chromatogram
1495.59
Search
Parameters
SampleSeparatio
n
DataAnalysis
Oligonucleotide
Adducts mixture
Ion pair Reversed
Phase
μ-HPLC-negative-ESI-
IT-MS Separation
GenoMass Software
Mass Spectrometry
data
Mobile Phase A: 100% 25mM
triethylammonium bicarbonate (TEAB), pH
8.43
, Mobile Phase B: 100% Methanol,
gradient: 5% to 50% MeOH in 23 min,
mixture of 30 pmol of each modified
oligonucleotide loaded onto the column.
Monolithic
column
μESI
(µL/min
)
PSDVB
0.25X100mm
5-6
GenoMass software is written in visual basic 6.0 under Windows
XP1
.
GenoMass software utilizes client-server architecture for
implementing the ‘reversed pseudo-combinatorial’ approach.
GenoMass is potentially a high-throughput computer software
capable of fast and efficient data mining of complex mass
spectrometric data for nucleic acid analysis.
GenoMass Software automate the data analysis by searching
input data file (LC-MS/MS data) for all possible base sequences
and their modified products.
14 mer 5’-PO4 –ACC CG1C G2TC CG3C G4C-3’OH,
(representing codons 156–159 of p53 gene), Oligonucleotides were
adducted with carcinogenic N-acetoxy-N-acetyl-2-aminofluorene
(AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP) by
previously described methods1,2
.
Unique isomer Mass ListUnique isomer Mass List
Built n-mer isomer mass
table on the fly if n<8 & Built
n-mer isomer mass table in
advance if n >9
Built n-mer isomer mass
table on the fly if n<8 & Built
n-mer isomer mass table in
advance if n >9
Convert raw file to
GenoMass format
Convert raw file to
GenoMass format
Flow charts of
GenoMass software
Flow charts of
GenoMass software
Tandemmassspectrometryinput
W,X,Y,Zseries
a,b,c,d,(a-B)series
SearchParametersSearchParameters
Gene SequenceGene Sequence
Load input fileLoad input file
Multi
charge
search
Run analysisRun analysis
Isomer type
(mer)
Isomer
containing
G/A/C/T
Adduct
search
LC/MS separation of oligonucleotide mixture using
monolithic column with the ion-pairing reagent (TEAB)
conditions
5’OH- TTT TTT TTT TTT TTT T -3’OH
van deemter H-u curve Average Pore size, 160.4 nm,
(Hagen-poiseuille law)
5’OH- TTTTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTTT -3’OH
5’OH- TTTTTTTTTTTTT -3’OH
ABP W9
5’-PO4 –ACC CG1 C G2TC CG3C G4C-
3’OH (a5-
B5)
AAAF
5’-PO4 –ACC CG1 CG2TC CG3C G4C-
3’OH (a5-B5)
W9
Input FileInput File
Results & DiscussionOverview
References
5’OH 3’OH
A high throughput screening method for identification of exact location of adducts on modified oligonucleotide ([ds 5’-PO4
-
-ACCCGCGTCCGCGC-3’/5’-GCGCGGGCGCGGGT-3’] modified
with adducts N-acetoxy-N-acetyl-2-aminofluorene (AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP))) is presented. The method is based on the tandem mass spectrometry aspect
of GenoMass software using ion pair reversed phase high performance liquid chromatography (IP-RP- -HPLC) via monolithic poly(styrene divinylbenzene) (PS DVB) capillaryμ μ − −
column coupled to electrospray ionization Ion Trap Mass Spectrometry (ESI-IT-MS).
A high throughput screening method for identification of exact location of adducts on modified oligonucleotide ([ds 5’-PO4
-
-ACCCGCGTCCGCGC-3’/5’-GCGCGGGCGCGGGT-3’] modified
with adducts N-acetoxy-N-acetyl-2-aminofluorene (AAAF) and N-hydroxy-4-aminobiphenyl (N-OH-4-ABP))) is presented. The method is based on the tandem mass spectrometry aspect
of GenoMass software using ion pair reversed phase high performance liquid chromatography (IP-RP- -HPLC) via monolithic poly(styrene divinylbenzene) (PS DVB) capillaryμ μ − −
column coupled to electrospray ionization Ion Trap Mass Spectrometry (ESI-IT-MS).
1) Liao, Q., Shen, C. and Vouros, P. (2009), GenoMass - a computer software for automated identification of oligonucleotide DNA adducts from LC-MS analysis of DNA digests.
Journal of Mass Spectrometry, 44: 549–560.
2) Chowdhury, G. and Guengerich, F. (2008), Direct Detection and Mapping of Sites of Base Modification in DNA Fragments by Tandem Mass Spectrometry. Angewandte Chemie
International Edition, 47: 381–384.
3) , Xiong, W., Glick, J,, Lin Y., and, Vouros. P. (2007), Separation and Sequencing of Isomeric Oligonucleotide Adducts Using Monolithic Columns by Ion-Pair Reversed-Phase
Nano-HPLC Coupled to Ion Trap Mass Spectrometry Analytical Chemistry 79 (14), 5312-5321.
4) Premstaller, A., Oberacher, H., Walcher, W., Timperio, A. M., Zolla, L., Chervet, J-P., Cavusoglu, N., Dorsselaer, A. V., and, Huber, C. G., (2001), High-Performance Liquid
Chromatography Electrospray Ionization Mass Spectrometry Using Monolithic Capillary Columns for Proteomic Studies,− Analytical Chemistry 73 (11), 2390-2396 This work was supported by grant from the National Institutes of Health RO169390
W2
-
W3
-
W4
-
W5
-
W6
-
W7
2-
W8
2-
W9
2-
W12
2-
856.65 1145.8
7
1474.7
9
1763.98 1026.58 1178.68 1343.28 1487.88 1941.67
(a13-
B13)2-
(a12-
B12)2-
(a11-
B11)2-
(a10-
B10)2-
(a9-
B9)2-
(a7-
B7)2-
(a6-
B6)-
(a5-B5)-
(a4-B4)-
1903.75 1759.17 1594.58 1449.97 1305.3
8
1977.38 1688.
16
1357.6
5
1069.7
7
W2
-
W3
-
W4
-
W5
-
W6
-
W7
2-
W8
2-
W9
2-
W11
2-
W12
2-
634.42 923.61 1252.79 1541.98 1831.67 1067.69 1232.28 1376.87 1770.58 1915.17
(a11-B11)2-
(a10-B10)2-
(a9-B9)2-
(a7-B7)2-
(a6-B6)-
(a5-B5)-
(a4-B4)-
1678.577 1533.97 1389.37 1072.68 1856.16 1357.73 1069.60
MS/MS
1495.59
MS/MS
1477.47
Load Input File for
(a5-B5)-
(Converted to
GenoMass format)
Conclusions
Load Input File for
W9
2-
(Converted to
GenoMass format)
N-hydroxy-4-aminobiphenyl
(N-OH-4-ABP)
modified 14 mer
N-acetoxy-N-acetyl-2-
aminofluorene (AAAF)
modified 14 mer
GenoMass
Software graphical
user interface
GenoMass
Software graphical
user interface
GenoMass is a unique software which connects tandem mass spectrometry (MS/MS) to a
combinatorial isomer library generated in silico for nucleotide <12 to identify a modified
Oligonucleotide and exact location of adduct.
GenoMass software correctly determines the existence of monoadducted positional isomers for ABP-
oligonucleotide, and AAAF-oligonucleotide.
Genomass software bridges the experimental MS/MS data and human genome database through
sequencing the modified oligonucleotides.
Acknowledgment](https://image.slidesharecdn.com/presentation1asms3-13248541076472-phpapp02-111225170325-phpapp02/85/ASMS_2011-1-320.jpg)
