Embed Size (px)
Citation preview
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMSKeeley Murphy1, Maciej Bromirski2, and Francois A. Espourteille1
1Thermo Fisher Scientific, San Jose , CA; 2Thermo Fisher Scientific, Bremen, Germany
2 High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS Keeley Murphy1; Maciej Bromirski2; Francois A. Espourteille1 ;1 Thermo Fisher Scientific, San Jose , CA; 2 Thermo Fisher Scientific, Bremen, Germany
Conclusion Liquid chromatography with high resolution mass spec analysis provided a robust
and reproducible method for high throughput screening and simultaneous analysis of multiple peptides at multiple charge states over the course of more that 3000 individual sample injections.
Full scan data collection across a wide mass range enabled the acquisition of spectral information for the entire isotopic charge envelope without sacrificing data quality.
Statistical analysis of a large injection set resulted in Z’ values ranging from 0.61 to 0.85 indicating method robustness the analysis.
Multiplexing using a four-LC channel system provided rapid injection cycle times of 30 seconds, on average, while proving separation from detergents and other interferences containing in sample matrixes.
Full Scan / Full Scan AIF data collection allows for simultaneous Full Scan quantitation as well MS/MS confirmation or quantitation with minimal reduction in instrument scan speed.
References1. Zhang,J.-H.; Chung,T.D.Y.; Oldenburg,K.R. J. Biomol. Screening 1999, 4, 67-73.
2. Roddy,T.P.; Horvath,C.R.; Stout,S.J. Anal. Chem. 2007, 79, 8207-8213.
OverviewPurpose: To implement high resolution accurate mass detection for the simultaneous analysis of multiple components in a high throughput screening assay.
Methods: Several peptides commonly monitored for cancer research were analyzed at various concentration levels in HEPES buffer solutions to determine signal response, linearity,-reproducibility, and Z’ value.
Results: Full scan mode at a resolving setting of 70,000 was utilized for the analysis of several thousand sample sets at cycle time of 30 seconds per sample. Four individual peptides were simultaneously analyzed with results demonstrating a linear signal response across the working range of the assay with analyte sensitivity in the low nM range. Full Scan operation at 70,000 resolving power enabled for data collection across a wide mass range allowing for multiple peptide monitoring at multiple charge states and detection of unexpected sample changes with no impact on instrument performance.
IntroductionLead discovery groups are constantly developing new methodologies to screen large chemical libraries against a specific target. The majority of these methods utilize plate reader devices, ELISA, and other analytical techniques that are amenable to high throughput analysis. Existing analytical methodology used for screening can be less than ideal due to sample prep considerations, limit of detection, and specificity of analyte detection. In these cases high resolution LCMS can provide a high quality alternative while maintaining a sampling rate that is suitable for HTS requirements. Liquid chromatography allows for analysis of samples in matrices that otherwise cause interference in the MS source, while high resolution MS provides sensitivity and specificity along with ease of use without compromising data quality. Two commercially available peptide sets commonly targeted for cancer research were analyzed in a simulated enzymatic screening assay experiment. Survivin 2B and Bid BH3 which are often targeted for analysis for their role in cell apoptosis were monitored at various concentrations in a high throughput screening experiment and the results analyzed to determine signal response, linearity,-reproducibility, and Z’ value.
MethodsSample Preparation
Five lyophilized peptides were ordered (catalog numbers: Survivin 2B (80-88) cat# 62693, Survivin (85-93) cat# 62691, Bid-BH3 cat# 61631, Bid BH3 (85-98) cat# 62485 and Substance P cat# 61694 from AnaSpec™, San Jose, CA). Each peptide was reconstituted in a deionized water at 1 mg/mL. Serial dilutions of Survivin and Bid-BH3 were prepared at concentrations of 1 nM, 5 nM, 10nM, 100 nM, and 1000 nM in in a 50 mM HEPES solution containing 50 mM MgCl2, 50mM Citric Acid, Tween20, and 1% (v/v) DMSO). Substance P was then added to each dilution level as an internal standard at a final concentration of 100 nM.
Liquid Chromatography and Multiplexing
Samples were injected onto a C18, 42.1 x 30 mm, 3.5 µm HPLC column. Analyte elution was accomplished using mobile phase A - water + 0.1% Formic Acid (v/v) and mobile phase B - Acetonitrile + 0.1% Formic Acid (v/v) with a 1-minute step gradient at a flow rate of 1.2 mL/min. The step gradient was performed at 0-10 sec, 2% B, 11-35 sec, 35%B, 36-65 sec, 95% B, and 66-100 sec, 5% B. All methods were completed using a Thermo Scientific Transcend LX-4 system with a dual injector arm with DLW (Dynamic Load and Wash). LC multiplexing was implemented with a data window of 18 seconds per LC channel.
Mass Spectrometry
A Thermo Scientific Exactive Plus bench-top Orbitrap mass spectrometer (Figure 1) was used in Full Scan and Full Scan all-ions-fragmentation (AIF). Full Scan data was collected across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz. A maximum inject time of 250ms for the Full Scan was applied. Full Scan AIF was collected with Full Scan across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz, and Full Scan AIF across a range of 200 – 2000 m/z at resolution of 17,500 and a spectral speed of 12 Hz using a Normalized Collision Energy of 25. A maximum inject time of 250ms was applied for the Full Scan with 50ms applied for the Full Scan AIF.
Ion source conditions were consistent for all MS experiment scan modes with the following parameters held constant, Vaporizer temperature 500°C, capillary temperature 375°C, sheath gas 60, and AUX gas 20. Prior to experimental data collection, the instrument was calibrated in positive ion mode using Pierce LTQ Velos ESI Positive Ion Calibration Solution.
FIGURE 1. Exactive Plus Instrument Schematic
AnaSpec is a trademark of AnaSpec, Inc. Gubbs is a trademark of Gubbs, Inc. Microsoft and Excel are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.
Sample sets were also collected using All Ion Fragment (AIF) to collect fragmentation spectra for all peptides present in the sample injection. The Full Scan was collected at a resolving power of 70,000 at 200m/z while the AIF was collected at a resolving power of 17,500 at 200m/z. The scans at the resolving power specified above allow for an average of 30 scans across the six second wide chromatographic peak. (Figure 4)
Samples in HEPES Buffer solution were analyzed at 5 concentration points ranging from 1nM to 1000nM with 288 replicate injections at each concentration level. The average peak area ratio was used to calculate %CV at each concentration and generate a calibration curve. (Table 1) The LOQ was determined to be 1nM for three peptides and 5nM for the fourth, with a linear signal response across the detected concentration range. Three of the peptides demonstrated a linear and reproducible response with %CVs below 20% at all concentration levels. The fourth peptide, although detectable at all concentration points displayed %CVs above 20% even at increasing concentration levels. Z-prime statistical analysis provides an indication of overall assay robustness based on the average and standard deviation of a positive and negative control. Z-prime values above 0.5 indicate a robust and acceptable assay. The z-prime for the forth peptide was well below 0.5 with a value of 0.32, indicating a lack of robustness in the analysis. Upon subsequent examination an unresolved interference was observed for the m/z of the fourth peptide that was not present during assay method development. The m/z collection range utilized in the full scan MS experiment allowed for reanalysis of the peptide at an alternate charge that provided an acceptable but lower signal response. The average, standard deviation, %CV, and z-prime was recalculated for the fourth peptide at the alternate charge state through re-interrogation of the previously collect data. (Figure 3)
In all runs, multiple sample injections were collected into a single data file format using Thermo Scientific Xcalibur and Aria software to automatically control data acquisition start and stop times for each sample set. Commercially available peptides were analyzed at various concentration levels and over multiple replicates to determine the coefficient of variation, linear response, and lower limit of quantitation. Results for each experiment type were compared for overall performance and ease of use.
Data Analysis SoftwareThermo Scientific Pinpoint software was used for exact mass calculation of all peptides at each of the observable charge states. Exact mass information was saved in Microsoft® Excel® for later use. Thermo Scientific QuickCalc software (powered by Gubbs Inc., GMSU Gubbs™ Mass Spec Utilities, Atlanta, GA) was used for all chromatographic data review, and report generation. Compound information was imported into QuickCalc™ software using an Excel import template containing the required m/z information. The compound information was stored in QuickCalc software for later use. The compound information was then grouped into a “compound set” and saved, allowing the exact m/z information for multiple compounds to be easily recalled and applied to an entire data set for easy chromatographic review. QuickCalc software was also used to automatically extract and sort each of the 96 injections contained in a data file and then display individual chromatographic peaks in a table view correlated with all sample information related to each individual injection.
Figure 5. Infusion of neat peptide solutions at 10uM conc. and resulting MSMS spectra
The fragmentation data collected during infusion was used to analyze AIF data collected during Full Scan analysis. The most intense fragmentations for each peptide were used to generate extracted ion chromatograms for the AIF data. The results demonstrate the presence of the expected fragmentation patterns for all peptides with scan speed, peak shape, retention time, and sensitivity adequate for MSMS confirmation as well accurate quantitation. The addition of the AIF did not affect the quantitative results of the Full Scan component of the experiment due to the rapid scanning speed of the MS.
FIGURE 4. AIF collection at 17,500 from 200-1000m/z. Scan settings provide for an average of 30 scans across the 6 second peak.
FIGURE 6. MSMS extracted ion chromatograms (XIC) for all four peptide in simultaneous analysis across a four channel multiplexing system. (Top) AIF XIC’s for each individual peptide across a four channel system. (Bottom) AIF spectra at chromatographic peak apex.
FIGURE 2. Top: Full scan peptide mix from 200 to 2000m/z. Bottom: zoomed scan range from 200 to 950m/z.
Full Scan data collection window
**Interference
Peptide Name Conc (nM)
Survivin 85-93
1 5 10 100 1000Avg. 0.012532 0.063424 0.135694 1.435063 12.96369
Std Dev 0.001733 0.007772 0.011968 0.16085 0.562784%CV 13.82914 12.25476 8.820187 11.20856 4.34123
z-prime 0.87
Survivin 2B 80-88
1 5 10 100 1000Avg. -- 0.005237 0.01118 0.133545 1.28023
Std Dev -- 0.000832 0.001688 0.019558 0.126222%CV -- 15.87972 15.0943 14.64532 9.859341
z-prime 0.71
Bid BH3 85-98
1 5 10 100 1000Avg. 0.00490 0.02708 0.05928 0.78428 7.52874
Std Dev 0.00094 0.004446 0.007849 0.097311 0.380001%CV 19.18882 16.41506 13.24001 12.4077 5.047339
z-prime 0.81
Bid BH3
1 5 10 100 1000Avg. 0.01718 0.04581 0.08430 0.62186 5.64208
Std Dev 0.003777 0.007009 0.01349 0.20801 2.483671%CV 21.98924 15.30206 16.00155 33.44948 44.0205
z-prime 0.32
Table 1. Mean, standard deviation, %CV and z-prime for each peptide analyzed. Highlighted values indicate %CV and z-prime values above acceptable levels.
FIGURE 3. Reanalysis of Bid BH3. (Top Left) Bid BH3 scans at +4 and +5, missing scans indicate deviation outside of 5ppm analysis window. (Top Right) MS spectra at +4, ∆ppm = 7.1 indicate an unresolved interference. (Bottom Left) MS spectra at +5, ∆ppm = 2.7. (Bottom Right) Table of recalculated Avg, Std. Dev., %CV, and z-prime.
52.55 52.60 52.65 52.70 52.75Time (min)
0
20
40
60
80
1000
20
40
60
80
100
Rel
ativ
e A
bund
ance
52.62
52.63
52.6352.64
52.65 52.66 52.68 52.70 52.7252.52 52.55 52.5952.61
52.61
52.6252.60
52.63
52.6452.60 52.66 52.7152.67 52.73 52.74 52.7652.57
T: FTMS + p ESI Full ms [350.00-615.00]
460.0 460.2 460.4 460.6 460.8 461.0 461.2 461.4 4m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
460.4938
460.7391
460.9855
461.2343
461.4847
460.2342459.9875
Peptide Name Conc (nM)
Bid BH3
1 5 10 100 1000Avg. -- 0.00039 0.00097 0.01210 0.11674
Std Dev -- 7.1E-05 0.000163 0.002023 0.012911
%CV 18.11 16.75 16.72451 11.05993
z-prime 0.61
Missing ScansBid BH3 +4
Bid BH3 +5
Bid BH3 +4
∆ppm = 2.7 Bid BH3 +5
Each peptide analyzed was interrogated for possible fragmentation prior to LC analysis. Neat solutions of each peptide were individually infused to determine the peptide fragmentation pattern. (Figure 5)
Bid BH3 85-98
Survivin 2B 80-88
Survivin 85-93
Bid BH3
Survivin 85-93
Survivin 80-88
Bid BH3 85-98
Bid BH3
ResultsTheoretical exact mass calculations were confirmed for each peptide by directly infusing with 1 μg/mL solution of each compound at 5 μL/min. (Figure 2) The charge states producing the most abundant signal for each peptide were determined during the infusion procedure and the mass range for the full scan experiment set accordingly to monitor all relevant charge states. Peptide charge states producing a low level response were excluded from the data collection window to reduce overall data file size, with all charge state ions below 10% of the total signal excluded from the collection range. Files containing 96 or more injections were limited to an overall size of less than 500MB.
F: FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
530.8096
680.2656
466.7800
508.2179
623.2443354.2084
779.3337344.8767 374.7192 580.3428
431.2611
290.1454
709.8824254.6124 890.3651789.3177 932.5519
FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
452.7581
588.3163
631.8318776.4509
502.2922904.5093
705.4138
530.8033388.7289
438.7608
948.4990353.2104 677.4188228.1338 1003.5778
876.5143339.2130
793.4769
762.4361
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
943.4174
624.2437
607.2169794.3123
693.2651 907.3964
711.2756523.1965 812.3231777.2831
638.2805
535.2717390.1436306.1443235.1074 506.1700
289.0960 889.3856386.1664881.3821 962.6227
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
200 400 600 800 1000 1200 1400 1600 1800 2000 2200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
943.4185613.6514932.4922
1067.6248 1409.6700 1527.7390 2012.27161737.0157
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
509.5845460.4916
943.4185613.6514 763.8723931.4894272.1717 597.8999 722.3664657.9211 766.9362368.5936
327.5356431.9845
368.2 368.4 368.6 368.8 369.0 369.2 369.4 369.6 369.8 370.0m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
368.5929
368.7933
368.9938
369.1942
369.3950368.1898 368.3896 369.2198 369.5966 369.9756368.8653
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
233.1645
257.1968
422.2392
550.3342
368.7208276.1339 571.3556736.4341
294.1443 443.2971
649.4022325.2048
589.3661
533.3080 719.4057849.5180746.4187
453.2812
896.2707
RT: 31.06 - 32.79 SM: 7B
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
50
100 0
50
1000
50
100
Rel
ativ
e A
bund
ance
0
50
100 NL: 1.26E6m/z= 422.2371-422.2413 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 6.34E5m/z= 624.2406-624.2468 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.83E6m/z= 631.8286-631.8350 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.57E6m/z= 680.2622-680.2690 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
613.6508
680.2655530.8094
508.2194
466.7798
623.2421
374.7191 594.3468 920.4725431.2617 779.3320354.2084
290.1460 763.8685931.4531
911.4638832.9104
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
20
40
60
80
1000 32.0432.0331.20 31.66
32.4631.6632.4531.6531.21 32.47
31.19 32.0532.0231.22 32.0531.65
32.44 32.4831.6831.1832.02
31.6431.22 32.06 32.4332.4931.23 31.69
31.73 32.0731.28 32.5431.63 32.01 32.4331.53 32.532.16
3Thermo Scientific Poster Note • PN63621_E 06/12S
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS Keeley Murphy1; Maciej Bromirski2; Francois A. Espourteille1 ;1 Thermo Fisher Scientific, San Jose , CA; 2 Thermo Fisher Scientific, Bremen, Germany
Conclusion Liquid chromatography with high resolution mass spec analysis provided a robust
and reproducible method for high throughput screening and simultaneous analysis of multiple peptides at multiple charge states over the course of more that 3000 individual sample injections.
Full scan data collection across a wide mass range enabled the acquisition of spectral information for the entire isotopic charge envelope without sacrificing data quality.
Statistical analysis of a large injection set resulted in Z’ values ranging from 0.61 to 0.85 indicating method robustness the analysis.
Multiplexing using a four-LC channel system provided rapid injection cycle times of 30 seconds, on average, while proving separation from detergents and other interferences containing in sample matrixes.
Full Scan / Full Scan AIF data collection allows for simultaneous Full Scan quantitation as well MS/MS confirmation or quantitation with minimal reduction in instrument scan speed.
References1. Zhang,J.-H.; Chung,T.D.Y.; Oldenburg,K.R. J. Biomol. Screening 1999, 4, 67-73.
2. Roddy,T.P.; Horvath,C.R.; Stout,S.J. Anal. Chem. 2007, 79, 8207-8213.
OverviewPurpose: To implement high resolution accurate mass detection for the simultaneous analysis of multiple components in a high throughput screening assay.
Methods: Several peptides commonly monitored for cancer research were analyzed at various concentration levels in HEPES buffer solutions to determine signal response, linearity,-reproducibility, and Z’ value.
Results: Full scan mode at a resolving setting of 70,000 was utilized for the analysis of several thousand sample sets at cycle time of 30 seconds per sample. Four individual peptides were simultaneously analyzed with results demonstrating a linear signal response across the working range of the assay with analyte sensitivity in the low nM range. Full Scan operation at 70,000 resolving power enabled for data collection across a wide mass range allowing for multiple peptide monitoring at multiple charge states and detection of unexpected sample changes with no impact on instrument performance.
IntroductionLead discovery groups are constantly developing new methodologies to screen large chemical libraries against a specific target. The majority of these methods utilize plate reader devices, ELISA, and other analytical techniques that are amenable to high throughput analysis. Existing analytical methodology used for screening can be less than ideal due to sample prep considerations, limit of detection, and specificity of analyte detection. In these cases high resolution LCMS can provide a high quality alternative while maintaining a sampling rate that is suitable for HTS requirements. Liquid chromatography allows for analysis of samples in matrices that otherwise cause interference in the MS source, while high resolution MS provides sensitivity and specificity along with ease of use without compromising data quality. Two commercially available peptide sets commonly targeted for cancer research were analyzed in a simulated enzymatic screening assay experiment. Survivin 2B and Bid BH3 which are often targeted for analysis for their role in cell apoptosis were monitored at various concentrations in a high throughput screening experiment and the results analyzed to determine signal response, linearity,-reproducibility, and Z’ value.
MethodsSample Preparation
Five lyophilized peptides were ordered (catalog numbers: Survivin 2B (80-88) cat# 62693, Survivin (85-93) cat# 62691, Bid-BH3 cat# 61631, Bid BH3 (85-98) cat# 62485 and Substance P cat# 61694 from AnaSpec™, San Jose, CA). Each peptide was reconstituted in a deionized water at 1 mg/mL. Serial dilutions of Survivin and Bid-BH3 were prepared at concentrations of 1 nM, 5 nM, 10nM, 100 nM, and 1000 nM in in a 50 mM HEPES solution containing 50 mM MgCl2, 50mM Citric Acid, Tween20, and 1% (v/v) DMSO). Substance P was then added to each dilution level as an internal standard at a final concentration of 100 nM.
Liquid Chromatography and Multiplexing
Samples were injected onto a C18, 42.1 x 30 mm, 3.5 µm HPLC column. Analyte elution was accomplished using mobile phase A - water + 0.1% Formic Acid (v/v) and mobile phase B - Acetonitrile + 0.1% Formic Acid (v/v) with a 1-minute step gradient at a flow rate of 1.2 mL/min. The step gradient was performed at 0-10 sec, 2% B, 11-35 sec, 35%B, 36-65 sec, 95% B, and 66-100 sec, 5% B. All methods were completed using a Thermo Scientific Transcend LX-4 system with a dual injector arm with DLW (Dynamic Load and Wash). LC multiplexing was implemented with a data window of 18 seconds per LC channel.
Mass Spectrometry
A Thermo Scientific Exactive Plus bench-top Orbitrap mass spectrometer (Figure 1) was used in Full Scan and Full Scan all-ions-fragmentation (AIF). Full Scan data was collected across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz. A maximum inject time of 250ms for the Full Scan was applied. Full Scan AIF was collected with Full Scan across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz, and Full Scan AIF across a range of 200 – 2000 m/z at resolution of 17,500 and a spectral speed of 12 Hz using a Normalized Collision Energy of 25. A maximum inject time of 250ms was applied for the Full Scan with 50ms applied for the Full Scan AIF.
Ion source conditions were consistent for all MS experiment scan modes with the following parameters held constant, Vaporizer temperature 500°C, capillary temperature 375°C, sheath gas 60, and AUX gas 20. Prior to experimental data collection, the instrument was calibrated in positive ion mode using Pierce LTQ Velos ESI Positive Ion Calibration Solution.
FIGURE 1. Exactive Plus Instrument Schematic
AnaSpec is a trademark of AnaSpec, Inc. Gubbs is a trademark of Gubbs, Inc. Microsoft and Excel are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.
Sample sets were also collected using All Ion Fragment (AIF) to collect fragmentation spectra for all peptides present in the sample injection. The Full Scan was collected at a resolving power of 70,000 at 200m/z while the AIF was collected at a resolving power of 17,500 at 200m/z. The scans at the resolving power specified above allow for an average of 30 scans across the six second wide chromatographic peak. (Figure 4)
Samples in HEPES Buffer solution were analyzed at 5 concentration points ranging from 1nM to 1000nM with 288 replicate injections at each concentration level. The average peak area ratio was used to calculate %CV at each concentration and generate a calibration curve. (Table 1) The LOQ was determined to be 1nM for three peptides and 5nM for the fourth, with a linear signal response across the detected concentration range. Three of the peptides demonstrated a linear and reproducible response with %CVs below 20% at all concentration levels. The fourth peptide, although detectable at all concentration points displayed %CVs above 20% even at increasing concentration levels. Z-prime statistical analysis provides an indication of overall assay robustness based on the average and standard deviation of a positive and negative control. Z-prime values above 0.5 indicate a robust and acceptable assay. The z-prime for the forth peptide was well below 0.5 with a value of 0.32, indicating a lack of robustness in the analysis. Upon subsequent examination an unresolved interference was observed for the m/z of the fourth peptide that was not present during assay method development. The m/z collection range utilized in the full scan MS experiment allowed for reanalysis of the peptide at an alternate charge that provided an acceptable but lower signal response. The average, standard deviation, %CV, and z-prime was recalculated for the fourth peptide at the alternate charge state through re-interrogation of the previously collect data. (Figure 3)
In all runs, multiple sample injections were collected into a single data file format using Thermo Scientific Xcalibur and Aria software to automatically control data acquisition start and stop times for each sample set. Commercially available peptides were analyzed at various concentration levels and over multiple replicates to determine the coefficient of variation, linear response, and lower limit of quantitation. Results for each experiment type were compared for overall performance and ease of use.
Data Analysis SoftwareThermo Scientific Pinpoint software was used for exact mass calculation of all peptides at each of the observable charge states. Exact mass information was saved in Microsoft® Excel® for later use. Thermo Scientific QuickCalc software (powered by Gubbs Inc., GMSU Gubbs™ Mass Spec Utilities, Atlanta, GA) was used for all chromatographic data review, and report generation. Compound information was imported into QuickCalc™ software using an Excel import template containing the required m/z information. The compound information was stored in QuickCalc software for later use. The compound information was then grouped into a “compound set” and saved, allowing the exact m/z information for multiple compounds to be easily recalled and applied to an entire data set for easy chromatographic review. QuickCalc software was also used to automatically extract and sort each of the 96 injections contained in a data file and then display individual chromatographic peaks in a table view correlated with all sample information related to each individual injection.
Figure 5. Infusion of neat peptide solutions at 10uM conc. and resulting MSMS spectra
The fragmentation data collected during infusion was used to analyze AIF data collected during Full Scan analysis. The most intense fragmentations for each peptide were used to generate extracted ion chromatograms for the AIF data. The results demonstrate the presence of the expected fragmentation patterns for all peptides with scan speed, peak shape, retention time, and sensitivity adequate for MSMS confirmation as well accurate quantitation. The addition of the AIF did not affect the quantitative results of the Full Scan component of the experiment due to the rapid scanning speed of the MS.
FIGURE 4. AIF collection at 17,500 from 200-1000m/z. Scan settings provide for an average of 30 scans across the 6 second peak.
FIGURE 6. MSMS extracted ion chromatograms (XIC) for all four peptide in simultaneous analysis across a four channel multiplexing system. (Top) AIF XIC’s for each individual peptide across a four channel system. (Bottom) AIF spectra at chromatographic peak apex.
FIGURE 2. Top: Full scan peptide mix from 200 to 2000m/z. Bottom: zoomed scan range from 200 to 950m/z.
Full Scan data collection window
**Interference
Peptide Name Conc (nM)
Survivin 85-93
1 5 10 100 1000Avg. 0.012532 0.063424 0.135694 1.435063 12.96369
Std Dev 0.001733 0.007772 0.011968 0.16085 0.562784%CV 13.82914 12.25476 8.820187 11.20856 4.34123
z-prime 0.87
Survivin 2B 80-88
1 5 10 100 1000Avg. -- 0.005237 0.01118 0.133545 1.28023
Std Dev -- 0.000832 0.001688 0.019558 0.126222%CV -- 15.87972 15.0943 14.64532 9.859341
z-prime 0.71
Bid BH3 85-98
1 5 10 100 1000Avg. 0.00490 0.02708 0.05928 0.78428 7.52874
Std Dev 0.00094 0.004446 0.007849 0.097311 0.380001%CV 19.18882 16.41506 13.24001 12.4077 5.047339
z-prime 0.81
Bid BH3
1 5 10 100 1000Avg. 0.01718 0.04581 0.08430 0.62186 5.64208
Std Dev 0.003777 0.007009 0.01349 0.20801 2.483671%CV 21.98924 15.30206 16.00155 33.44948 44.0205
z-prime 0.32
Table 1. Mean, standard deviation, %CV and z-prime for each peptide analyzed. Highlighted values indicate %CV and z-prime values above acceptable levels.
FIGURE 3. Reanalysis of Bid BH3. (Top Left) Bid BH3 scans at +4 and +5, missing scans indicate deviation outside of 5ppm analysis window. (Top Right) MS spectra at +4, ∆ppm = 7.1 indicate an unresolved interference. (Bottom Left) MS spectra at +5, ∆ppm = 2.7. (Bottom Right) Table of recalculated Avg, Std. Dev., %CV, and z-prime.
52.55 52.60 52.65 52.70 52.75Time (min)
0
20
40
60
80
1000
20
40
60
80
100
Rel
ativ
e A
bund
ance
52.62
52.63
52.6352.64
52.65 52.66 52.68 52.70 52.7252.52 52.55 52.5952.61
52.61
52.6252.60
52.63
52.6452.60 52.66 52.7152.67 52.73 52.74 52.7652.57
T: FTMS + p ESI Full ms [350.00-615.00]
460.0 460.2 460.4 460.6 460.8 461.0 461.2 461.4 4m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
460.4938
460.7391
460.9855
461.2343
461.4847
460.2342459.9875
Peptide Name Conc (nM)
Bid BH3
1 5 10 100 1000Avg. -- 0.00039 0.00097 0.01210 0.11674
Std Dev -- 7.1E-05 0.000163 0.002023 0.012911
%CV 18.11 16.75 16.72451 11.05993
z-prime 0.61
Missing ScansBid BH3 +4
Bid BH3 +5
Bid BH3 +4
∆ppm = 2.7 Bid BH3 +5
Each peptide analyzed was interrogated for possible fragmentation prior to LC analysis. Neat solutions of each peptide were individually infused to determine the peptide fragmentation pattern. (Figure 5)
Bid BH3 85-98
Survivin 2B 80-88
Survivin 85-93
Bid BH3
Survivin 85-93
Survivin 80-88
Bid BH3 85-98
Bid BH3
ResultsTheoretical exact mass calculations were confirmed for each peptide by directly infusing with 1 μg/mL solution of each compound at 5 μL/min. (Figure 2) The charge states producing the most abundant signal for each peptide were determined during the infusion procedure and the mass range for the full scan experiment set accordingly to monitor all relevant charge states. Peptide charge states producing a low level response were excluded from the data collection window to reduce overall data file size, with all charge state ions below 10% of the total signal excluded from the collection range. Files containing 96 or more injections were limited to an overall size of less than 500MB.
F: FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
530.8096
680.2656
466.7800
508.2179
623.2443354.2084
779.3337344.8767 374.7192 580.3428
431.2611
290.1454
709.8824254.6124 890.3651789.3177 932.5519
FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
452.7581
588.3163
631.8318776.4509
502.2922904.5093
705.4138
530.8033388.7289
438.7608
948.4990353.2104 677.4188228.1338 1003.5778
876.5143339.2130
793.4769
762.4361
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
943.4174
624.2437
607.2169794.3123
693.2651 907.3964
711.2756523.1965 812.3231777.2831
638.2805
535.2717390.1436306.1443235.1074 506.1700
289.0960 889.3856386.1664881.3821 962.6227
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
200 400 600 800 1000 1200 1400 1600 1800 2000 2200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
943.4185613.6514932.4922
1067.6248 1409.6700 1527.7390 2012.27161737.0157
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
509.5845460.4916
943.4185613.6514 763.8723931.4894272.1717 597.8999 722.3664657.9211 766.9362368.5936
327.5356431.9845
368.2 368.4 368.6 368.8 369.0 369.2 369.4 369.6 369.8 370.0m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
368.5929
368.7933
368.9938
369.1942
369.3950368.1898 368.3896 369.2198 369.5966 369.9756368.8653
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
233.1645
257.1968
422.2392
550.3342
368.7208276.1339 571.3556736.4341
294.1443 443.2971
649.4022325.2048
589.3661
533.3080 719.4057849.5180746.4187
453.2812
896.2707
RT: 31.06 - 32.79 SM: 7B
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
50
100 0
50
1000
50
100
Rel
ativ
e A
bund
ance
0
50
100 NL: 1.26E6m/z= 422.2371-422.2413 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 6.34E5m/z= 624.2406-624.2468 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.83E6m/z= 631.8286-631.8350 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.57E6m/z= 680.2622-680.2690 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
613.6508
680.2655530.8094
508.2194
466.7798
623.2421
374.7191 594.3468 920.4725431.2617 779.3320354.2084
290.1460 763.8685931.4531
911.4638832.9104
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
20
40
60
80
1000 32.0432.0331.20 31.66
32.4631.6632.4531.6531.21 32.47
31.19 32.0532.0231.22 32.0531.65
32.44 32.4831.6831.1832.02
31.6431.22 32.06 32.4332.4931.23 31.69
31.73 32.0731.28 32.5431.63 32.01 32.4331.53 32.532.16
4 High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS Keeley Murphy1; Maciej Bromirski2; Francois A. Espourteille1 ;1 Thermo Fisher Scientific, San Jose , CA; 2 Thermo Fisher Scientific, Bremen, Germany
Conclusion Liquid chromatography with high resolution mass spec analysis provided a robust
and reproducible method for high throughput screening and simultaneous analysis of multiple peptides at multiple charge states over the course of more that 3000 individual sample injections.
Full scan data collection across a wide mass range enabled the acquisition of spectral information for the entire isotopic charge envelope without sacrificing data quality.
Statistical analysis of a large injection set resulted in Z’ values ranging from 0.61 to 0.85 indicating method robustness the analysis.
Multiplexing using a four-LC channel system provided rapid injection cycle times of 30 seconds, on average, while proving separation from detergents and other interferences containing in sample matrixes.
Full Scan / Full Scan AIF data collection allows for simultaneous Full Scan quantitation as well MS/MS confirmation or quantitation with minimal reduction in instrument scan speed.
References1. Zhang,J.-H.; Chung,T.D.Y.; Oldenburg,K.R. J. Biomol. Screening 1999, 4, 67-73.
2. Roddy,T.P.; Horvath,C.R.; Stout,S.J. Anal. Chem. 2007, 79, 8207-8213.
OverviewPurpose: To implement high resolution accurate mass detection for the simultaneous analysis of multiple components in a high throughput screening assay.
Methods: Several peptides commonly monitored for cancer research were analyzed at various concentration levels in HEPES buffer solutions to determine signal response, linearity,-reproducibility, and Z’ value.
Results: Full scan mode at a resolving setting of 70,000 was utilized for the analysis of several thousand sample sets at cycle time of 30 seconds per sample. Four individual peptides were simultaneously analyzed with results demonstrating a linear signal response across the working range of the assay with analyte sensitivity in the low nM range. Full Scan operation at 70,000 resolving power enabled for data collection across a wide mass range allowing for multiple peptide monitoring at multiple charge states and detection of unexpected sample changes with no impact on instrument performance.
IntroductionLead discovery groups are constantly developing new methodologies to screen large chemical libraries against a specific target. The majority of these methods utilize plate reader devices, ELISA, and other analytical techniques that are amenable to high throughput analysis. Existing analytical methodology used for screening can be less than ideal due to sample prep considerations, limit of detection, and specificity of analyte detection. In these cases high resolution LCMS can provide a high quality alternative while maintaining a sampling rate that is suitable for HTS requirements. Liquid chromatography allows for analysis of samples in matrices that otherwise cause interference in the MS source, while high resolution MS provides sensitivity and specificity along with ease of use without compromising data quality. Two commercially available peptide sets commonly targeted for cancer research were analyzed in a simulated enzymatic screening assay experiment. Survivin 2B and Bid BH3 which are often targeted for analysis for their role in cell apoptosis were monitored at various concentrations in a high throughput screening experiment and the results analyzed to determine signal response, linearity,-reproducibility, and Z’ value.
MethodsSample Preparation
Five lyophilized peptides were ordered (catalog numbers: Survivin 2B (80-88) cat# 62693, Survivin (85-93) cat# 62691, Bid-BH3 cat# 61631, Bid BH3 (85-98) cat# 62485 and Substance P cat# 61694 from AnaSpec™, San Jose, CA). Each peptide was reconstituted in a deionized water at 1 mg/mL. Serial dilutions of Survivin and Bid-BH3 were prepared at concentrations of 1 nM, 5 nM, 10nM, 100 nM, and 1000 nM in in a 50 mM HEPES solution containing 50 mM MgCl2, 50mM Citric Acid, Tween20, and 1% (v/v) DMSO). Substance P was then added to each dilution level as an internal standard at a final concentration of 100 nM.
Liquid Chromatography and Multiplexing
Samples were injected onto a C18, 42.1 x 30 mm, 3.5 µm HPLC column. Analyte elution was accomplished using mobile phase A - water + 0.1% Formic Acid (v/v) and mobile phase B - Acetonitrile + 0.1% Formic Acid (v/v) with a 1-minute step gradient at a flow rate of 1.2 mL/min. The step gradient was performed at 0-10 sec, 2% B, 11-35 sec, 35%B, 36-65 sec, 95% B, and 66-100 sec, 5% B. All methods were completed using a Thermo Scientific Transcend LX-4 system with a dual injector arm with DLW (Dynamic Load and Wash). LC multiplexing was implemented with a data window of 18 seconds per LC channel.
Mass Spectrometry
A Thermo Scientific Exactive Plus bench-top Orbitrap mass spectrometer (Figure 1) was used in Full Scan and Full Scan all-ions-fragmentation (AIF). Full Scan data was collected across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz. A maximum inject time of 250ms for the Full Scan was applied. Full Scan AIF was collected with Full Scan across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz, and Full Scan AIF across a range of 200 – 2000 m/z at resolution of 17,500 and a spectral speed of 12 Hz using a Normalized Collision Energy of 25. A maximum inject time of 250ms was applied for the Full Scan with 50ms applied for the Full Scan AIF.
Ion source conditions were consistent for all MS experiment scan modes with the following parameters held constant, Vaporizer temperature 500°C, capillary temperature 375°C, sheath gas 60, and AUX gas 20. Prior to experimental data collection, the instrument was calibrated in positive ion mode using Pierce LTQ Velos ESI Positive Ion Calibration Solution.
FIGURE 1. Exactive Plus Instrument Schematic
AnaSpec is a trademark of AnaSpec, Inc. Gubbs is a trademark of Gubbs, Inc. Microsoft and Excel are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.
Sample sets were also collected using All Ion Fragment (AIF) to collect fragmentation spectra for all peptides present in the sample injection. The Full Scan was collected at a resolving power of 70,000 at 200m/z while the AIF was collected at a resolving power of 17,500 at 200m/z. The scans at the resolving power specified above allow for an average of 30 scans across the six second wide chromatographic peak. (Figure 4)
Samples in HEPES Buffer solution were analyzed at 5 concentration points ranging from 1nM to 1000nM with 288 replicate injections at each concentration level. The average peak area ratio was used to calculate %CV at each concentration and generate a calibration curve. (Table 1) The LOQ was determined to be 1nM for three peptides and 5nM for the fourth, with a linear signal response across the detected concentration range. Three of the peptides demonstrated a linear and reproducible response with %CVs below 20% at all concentration levels. The fourth peptide, although detectable at all concentration points displayed %CVs above 20% even at increasing concentration levels. Z-prime statistical analysis provides an indication of overall assay robustness based on the average and standard deviation of a positive and negative control. Z-prime values above 0.5 indicate a robust and acceptable assay. The z-prime for the forth peptide was well below 0.5 with a value of 0.32, indicating a lack of robustness in the analysis. Upon subsequent examination an unresolved interference was observed for the m/z of the fourth peptide that was not present during assay method development. The m/z collection range utilized in the full scan MS experiment allowed for reanalysis of the peptide at an alternate charge that provided an acceptable but lower signal response. The average, standard deviation, %CV, and z-prime was recalculated for the fourth peptide at the alternate charge state through re-interrogation of the previously collect data. (Figure 3)
In all runs, multiple sample injections were collected into a single data file format using Thermo Scientific Xcalibur and Aria software to automatically control data acquisition start and stop times for each sample set. Commercially available peptides were analyzed at various concentration levels and over multiple replicates to determine the coefficient of variation, linear response, and lower limit of quantitation. Results for each experiment type were compared for overall performance and ease of use.
Data Analysis SoftwareThermo Scientific Pinpoint software was used for exact mass calculation of all peptides at each of the observable charge states. Exact mass information was saved in Microsoft® Excel® for later use. Thermo Scientific QuickCalc software (powered by Gubbs Inc., GMSU Gubbs™ Mass Spec Utilities, Atlanta, GA) was used for all chromatographic data review, and report generation. Compound information was imported into QuickCalc™ software using an Excel import template containing the required m/z information. The compound information was stored in QuickCalc software for later use. The compound information was then grouped into a “compound set” and saved, allowing the exact m/z information for multiple compounds to be easily recalled and applied to an entire data set for easy chromatographic review. QuickCalc software was also used to automatically extract and sort each of the 96 injections contained in a data file and then display individual chromatographic peaks in a table view correlated with all sample information related to each individual injection.
Figure 5. Infusion of neat peptide solutions at 10uM conc. and resulting MSMS spectra
The fragmentation data collected during infusion was used to analyze AIF data collected during Full Scan analysis. The most intense fragmentations for each peptide were used to generate extracted ion chromatograms for the AIF data. The results demonstrate the presence of the expected fragmentation patterns for all peptides with scan speed, peak shape, retention time, and sensitivity adequate for MSMS confirmation as well accurate quantitation. The addition of the AIF did not affect the quantitative results of the Full Scan component of the experiment due to the rapid scanning speed of the MS.
FIGURE 4. AIF collection at 17,500 from 200-1000m/z. Scan settings provide for an average of 30 scans across the 6 second peak.
FIGURE 6. MSMS extracted ion chromatograms (XIC) for all four peptide in simultaneous analysis across a four channel multiplexing system. (Top) AIF XIC’s for each individual peptide across a four channel system. (Bottom) AIF spectra at chromatographic peak apex.
FIGURE 2. Top: Full scan peptide mix from 200 to 2000m/z. Bottom: zoomed scan range from 200 to 950m/z.
Full Scan data collection window
**Interference
Peptide Name Conc (nM)
Survivin 85-93
1 5 10 100 1000Avg. 0.012532 0.063424 0.135694 1.435063 12.96369
Std Dev 0.001733 0.007772 0.011968 0.16085 0.562784%CV 13.82914 12.25476 8.820187 11.20856 4.34123
z-prime 0.87
Survivin 2B 80-88
1 5 10 100 1000Avg. -- 0.005237 0.01118 0.133545 1.28023
Std Dev -- 0.000832 0.001688 0.019558 0.126222%CV -- 15.87972 15.0943 14.64532 9.859341
z-prime 0.71
Bid BH3 85-98
1 5 10 100 1000Avg. 0.00490 0.02708 0.05928 0.78428 7.52874
Std Dev 0.00094 0.004446 0.007849 0.097311 0.380001%CV 19.18882 16.41506 13.24001 12.4077 5.047339
z-prime 0.81
Bid BH3
1 5 10 100 1000Avg. 0.01718 0.04581 0.08430 0.62186 5.64208
Std Dev 0.003777 0.007009 0.01349 0.20801 2.483671%CV 21.98924 15.30206 16.00155 33.44948 44.0205
z-prime 0.32
Table 1. Mean, standard deviation, %CV and z-prime for each peptide analyzed. Highlighted values indicate %CV and z-prime values above acceptable levels.
FIGURE 3. Reanalysis of Bid BH3. (Top Left) Bid BH3 scans at +4 and +5, missing scans indicate deviation outside of 5ppm analysis window. (Top Right) MS spectra at +4, ∆ppm = 7.1 indicate an unresolved interference. (Bottom Left) MS spectra at +5, ∆ppm = 2.7. (Bottom Right) Table of recalculated Avg, Std. Dev., %CV, and z-prime.
52.55 52.60 52.65 52.70 52.75Time (min)
0
20
40
60
80
1000
20
40
60
80
100
Rel
ativ
e A
bund
ance
52.62
52.63
52.6352.64
52.65 52.66 52.68 52.70 52.7252.52 52.55 52.5952.61
52.61
52.6252.60
52.63
52.6452.60 52.66 52.7152.67 52.73 52.74 52.7652.57
T: FTMS + p ESI Full ms [350.00-615.00]
460.0 460.2 460.4 460.6 460.8 461.0 461.2 461.4 4m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
460.4938
460.7391
460.9855
461.2343
461.4847
460.2342459.9875
Peptide Name Conc (nM)
Bid BH3
1 5 10 100 1000Avg. -- 0.00039 0.00097 0.01210 0.11674
Std Dev -- 7.1E-05 0.000163 0.002023 0.012911
%CV 18.11 16.75 16.72451 11.05993
z-prime 0.61
Missing ScansBid BH3 +4
Bid BH3 +5
Bid BH3 +4
∆ppm = 2.7 Bid BH3 +5
Each peptide analyzed was interrogated for possible fragmentation prior to LC analysis. Neat solutions of each peptide were individually infused to determine the peptide fragmentation pattern. (Figure 5)
Bid BH3 85-98
Survivin 2B 80-88
Survivin 85-93
Bid BH3
Survivin 85-93
Survivin 80-88
Bid BH3 85-98
Bid BH3
ResultsTheoretical exact mass calculations were confirmed for each peptide by directly infusing with 1 μg/mL solution of each compound at 5 μL/min. (Figure 2) The charge states producing the most abundant signal for each peptide were determined during the infusion procedure and the mass range for the full scan experiment set accordingly to monitor all relevant charge states. Peptide charge states producing a low level response were excluded from the data collection window to reduce overall data file size, with all charge state ions below 10% of the total signal excluded from the collection range. Files containing 96 or more injections were limited to an overall size of less than 500MB.
F: FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
530.8096
680.2656
466.7800
508.2179
623.2443354.2084
779.3337344.8767 374.7192 580.3428
431.2611
290.1454
709.8824254.6124 890.3651789.3177 932.5519
FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
452.7581
588.3163
631.8318776.4509
502.2922904.5093
705.4138
530.8033388.7289
438.7608
948.4990353.2104 677.4188228.1338 1003.5778
876.5143339.2130
793.4769
762.4361
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
943.4174
624.2437
607.2169794.3123
693.2651 907.3964
711.2756523.1965 812.3231777.2831
638.2805
535.2717390.1436306.1443235.1074 506.1700
289.0960 889.3856386.1664881.3821 962.6227
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
200 400 600 800 1000 1200 1400 1600 1800 2000 2200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
943.4185613.6514932.4922
1067.6248 1409.6700 1527.7390 2012.27161737.0157
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
509.5845460.4916
943.4185613.6514 763.8723931.4894272.1717 597.8999 722.3664657.9211 766.9362368.5936
327.5356431.9845
368.2 368.4 368.6 368.8 369.0 369.2 369.4 369.6 369.8 370.0m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
368.5929
368.7933
368.9938
369.1942
369.3950368.1898 368.3896 369.2198 369.5966 369.9756368.8653
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
233.1645
257.1968
422.2392
550.3342
368.7208276.1339 571.3556736.4341
294.1443 443.2971
649.4022325.2048
589.3661
533.3080 719.4057849.5180746.4187
453.2812
896.2707
RT: 31.06 - 32.79 SM: 7B
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
50
100 0
50
1000
50
100
Rel
ativ
e A
bund
ance
0
50
100 NL: 1.26E6m/z= 422.2371-422.2413 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 6.34E5m/z= 624.2406-624.2468 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.83E6m/z= 631.8286-631.8350 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.57E6m/z= 680.2622-680.2690 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
613.6508
680.2655530.8094
508.2194
466.7798
623.2421
374.7191 594.3468 920.4725431.2617 779.3320354.2084
290.1460 763.8685931.4531
911.4638832.9104
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
20
40
60
80
1000 32.0432.0331.20 31.66
32.4631.6632.4531.6531.21 32.47
31.19 32.0532.0231.22 32.0531.65
32.44 32.4831.6831.1832.02
31.6431.22 32.06 32.4332.4931.23 31.69
31.73 32.0731.28 32.5431.63 32.01 32.4331.53 32.532.16
5Thermo Scientific Poster Note • PN63621_E 06/12S
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS Keeley Murphy1; Maciej Bromirski2; Francois A. Espourteille1 ;1 Thermo Fisher Scientific, San Jose , CA; 2 Thermo Fisher Scientific, Bremen, Germany
Conclusion Liquid chromatography with high resolution mass spec analysis provided a robust
and reproducible method for high throughput screening and simultaneous analysis of multiple peptides at multiple charge states over the course of more that 3000 individual sample injections.
Full scan data collection across a wide mass range enabled the acquisition of spectral information for the entire isotopic charge envelope without sacrificing data quality.
Statistical analysis of a large injection set resulted in Z’ values ranging from 0.61 to 0.85 indicating method robustness the analysis.
Multiplexing using a four-LC channel system provided rapid injection cycle times of 30 seconds, on average, while proving separation from detergents and other interferences containing in sample matrixes.
Full Scan / Full Scan AIF data collection allows for simultaneous Full Scan quantitation as well MS/MS confirmation or quantitation with minimal reduction in instrument scan speed.
References1. Zhang,J.-H.; Chung,T.D.Y.; Oldenburg,K.R. J. Biomol. Screening 1999, 4, 67-73.
2. Roddy,T.P.; Horvath,C.R.; Stout,S.J. Anal. Chem. 2007, 79, 8207-8213.
OverviewPurpose: To implement high resolution accurate mass detection for the simultaneous analysis of multiple components in a high throughput screening assay.
Methods: Several peptides commonly monitored for cancer research were analyzed at various concentration levels in HEPES buffer solutions to determine signal response, linearity,-reproducibility, and Z’ value.
Results: Full scan mode at a resolving setting of 70,000 was utilized for the analysis of several thousand sample sets at cycle time of 30 seconds per sample. Four individual peptides were simultaneously analyzed with results demonstrating a linear signal response across the working range of the assay with analyte sensitivity in the low nM range. Full Scan operation at 70,000 resolving power enabled for data collection across a wide mass range allowing for multiple peptide monitoring at multiple charge states and detection of unexpected sample changes with no impact on instrument performance.
IntroductionLead discovery groups are constantly developing new methodologies to screen large chemical libraries against a specific target. The majority of these methods utilize plate reader devices, ELISA, and other analytical techniques that are amenable to high throughput analysis. Existing analytical methodology used for screening can be less than ideal due to sample prep considerations, limit of detection, and specificity of analyte detection. In these cases high resolution LCMS can provide a high quality alternative while maintaining a sampling rate that is suitable for HTS requirements. Liquid chromatography allows for analysis of samples in matrices that otherwise cause interference in the MS source, while high resolution MS provides sensitivity and specificity along with ease of use without compromising data quality. Two commercially available peptide sets commonly targeted for cancer research were analyzed in a simulated enzymatic screening assay experiment. Survivin 2B and Bid BH3 which are often targeted for analysis for their role in cell apoptosis were monitored at various concentrations in a high throughput screening experiment and the results analyzed to determine signal response, linearity,-reproducibility, and Z’ value.
MethodsSample Preparation
Five lyophilized peptides were ordered (catalog numbers: Survivin 2B (80-88) cat# 62693, Survivin (85-93) cat# 62691, Bid-BH3 cat# 61631, Bid BH3 (85-98) cat# 62485 and Substance P cat# 61694 from AnaSpec™, San Jose, CA). Each peptide was reconstituted in a deionized water at 1 mg/mL. Serial dilutions of Survivin and Bid-BH3 were prepared at concentrations of 1 nM, 5 nM, 10nM, 100 nM, and 1000 nM in in a 50 mM HEPES solution containing 50 mM MgCl2, 50mM Citric Acid, Tween20, and 1% (v/v) DMSO). Substance P was then added to each dilution level as an internal standard at a final concentration of 100 nM.
Liquid Chromatography and Multiplexing
Samples were injected onto a C18, 42.1 x 30 mm, 3.5 µm HPLC column. Analyte elution was accomplished using mobile phase A - water + 0.1% Formic Acid (v/v) and mobile phase B - Acetonitrile + 0.1% Formic Acid (v/v) with a 1-minute step gradient at a flow rate of 1.2 mL/min. The step gradient was performed at 0-10 sec, 2% B, 11-35 sec, 35%B, 36-65 sec, 95% B, and 66-100 sec, 5% B. All methods were completed using a Thermo Scientific Transcend LX-4 system with a dual injector arm with DLW (Dynamic Load and Wash). LC multiplexing was implemented with a data window of 18 seconds per LC channel.
Mass Spectrometry
A Thermo Scientific Exactive Plus bench-top Orbitrap mass spectrometer (Figure 1) was used in Full Scan and Full Scan all-ions-fragmentation (AIF). Full Scan data was collected across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz. A maximum inject time of 250ms for the Full Scan was applied. Full Scan AIF was collected with Full Scan across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz, and Full Scan AIF across a range of 200 – 2000 m/z at resolution of 17,500 and a spectral speed of 12 Hz using a Normalized Collision Energy of 25. A maximum inject time of 250ms was applied for the Full Scan with 50ms applied for the Full Scan AIF.
Ion source conditions were consistent for all MS experiment scan modes with the following parameters held constant, Vaporizer temperature 500°C, capillary temperature 375°C, sheath gas 60, and AUX gas 20. Prior to experimental data collection, the instrument was calibrated in positive ion mode using Pierce LTQ Velos ESI Positive Ion Calibration Solution.
FIGURE 1. Exactive Plus Instrument Schematic
AnaSpec is a trademark of AnaSpec, Inc. Gubbs is a trademark of Gubbs, Inc. Microsoft and Excel are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.
Sample sets were also collected using All Ion Fragment (AIF) to collect fragmentation spectra for all peptides present in the sample injection. The Full Scan was collected at a resolving power of 70,000 at 200m/z while the AIF was collected at a resolving power of 17,500 at 200m/z. The scans at the resolving power specified above allow for an average of 30 scans across the six second wide chromatographic peak. (Figure 4)
Samples in HEPES Buffer solution were analyzed at 5 concentration points ranging from 1nM to 1000nM with 288 replicate injections at each concentration level. The average peak area ratio was used to calculate %CV at each concentration and generate a calibration curve. (Table 1) The LOQ was determined to be 1nM for three peptides and 5nM for the fourth, with a linear signal response across the detected concentration range. Three of the peptides demonstrated a linear and reproducible response with %CVs below 20% at all concentration levels. The fourth peptide, although detectable at all concentration points displayed %CVs above 20% even at increasing concentration levels. Z-prime statistical analysis provides an indication of overall assay robustness based on the average and standard deviation of a positive and negative control. Z-prime values above 0.5 indicate a robust and acceptable assay. The z-prime for the forth peptide was well below 0.5 with a value of 0.32, indicating a lack of robustness in the analysis. Upon subsequent examination an unresolved interference was observed for the m/z of the fourth peptide that was not present during assay method development. The m/z collection range utilized in the full scan MS experiment allowed for reanalysis of the peptide at an alternate charge that provided an acceptable but lower signal response. The average, standard deviation, %CV, and z-prime was recalculated for the fourth peptide at the alternate charge state through re-interrogation of the previously collect data. (Figure 3)
In all runs, multiple sample injections were collected into a single data file format using Thermo Scientific Xcalibur and Aria software to automatically control data acquisition start and stop times for each sample set. Commercially available peptides were analyzed at various concentration levels and over multiple replicates to determine the coefficient of variation, linear response, and lower limit of quantitation. Results for each experiment type were compared for overall performance and ease of use.
Data Analysis SoftwareThermo Scientific Pinpoint software was used for exact mass calculation of all peptides at each of the observable charge states. Exact mass information was saved in Microsoft® Excel® for later use. Thermo Scientific QuickCalc software (powered by Gubbs Inc., GMSU Gubbs™ Mass Spec Utilities, Atlanta, GA) was used for all chromatographic data review, and report generation. Compound information was imported into QuickCalc™ software using an Excel import template containing the required m/z information. The compound information was stored in QuickCalc software for later use. The compound information was then grouped into a “compound set” and saved, allowing the exact m/z information for multiple compounds to be easily recalled and applied to an entire data set for easy chromatographic review. QuickCalc software was also used to automatically extract and sort each of the 96 injections contained in a data file and then display individual chromatographic peaks in a table view correlated with all sample information related to each individual injection.
Figure 5. Infusion of neat peptide solutions at 10uM conc. and resulting MSMS spectra
The fragmentation data collected during infusion was used to analyze AIF data collected during Full Scan analysis. The most intense fragmentations for each peptide were used to generate extracted ion chromatograms for the AIF data. The results demonstrate the presence of the expected fragmentation patterns for all peptides with scan speed, peak shape, retention time, and sensitivity adequate for MSMS confirmation as well accurate quantitation. The addition of the AIF did not affect the quantitative results of the Full Scan component of the experiment due to the rapid scanning speed of the MS.
FIGURE 4. AIF collection at 17,500 from 200-1000m/z. Scan settings provide for an average of 30 scans across the 6 second peak.
FIGURE 6. MSMS extracted ion chromatograms (XIC) for all four peptide in simultaneous analysis across a four channel multiplexing system. (Top) AIF XIC’s for each individual peptide across a four channel system. (Bottom) AIF spectra at chromatographic peak apex.
FIGURE 2. Top: Full scan peptide mix from 200 to 2000m/z. Bottom: zoomed scan range from 200 to 950m/z.
Full Scan data collection window
**Interference
Peptide Name Conc (nM)
Survivin 85-93
1 5 10 100 1000Avg. 0.012532 0.063424 0.135694 1.435063 12.96369
Std Dev 0.001733 0.007772 0.011968 0.16085 0.562784%CV 13.82914 12.25476 8.820187 11.20856 4.34123
z-prime 0.87
Survivin 2B 80-88
1 5 10 100 1000Avg. -- 0.005237 0.01118 0.133545 1.28023
Std Dev -- 0.000832 0.001688 0.019558 0.126222%CV -- 15.87972 15.0943 14.64532 9.859341
z-prime 0.71
Bid BH3 85-98
1 5 10 100 1000Avg. 0.00490 0.02708 0.05928 0.78428 7.52874
Std Dev 0.00094 0.004446 0.007849 0.097311 0.380001%CV 19.18882 16.41506 13.24001 12.4077 5.047339
z-prime 0.81
Bid BH3
1 5 10 100 1000Avg. 0.01718 0.04581 0.08430 0.62186 5.64208
Std Dev 0.003777 0.007009 0.01349 0.20801 2.483671%CV 21.98924 15.30206 16.00155 33.44948 44.0205
z-prime 0.32
Table 1. Mean, standard deviation, %CV and z-prime for each peptide analyzed. Highlighted values indicate %CV and z-prime values above acceptable levels.
FIGURE 3. Reanalysis of Bid BH3. (Top Left) Bid BH3 scans at +4 and +5, missing scans indicate deviation outside of 5ppm analysis window. (Top Right) MS spectra at +4, ∆ppm = 7.1 indicate an unresolved interference. (Bottom Left) MS spectra at +5, ∆ppm = 2.7. (Bottom Right) Table of recalculated Avg, Std. Dev., %CV, and z-prime.
52.55 52.60 52.65 52.70 52.75Time (min)
0
20
40
60
80
1000
20
40
60
80
100
Rel
ativ
e A
bund
ance
52.62
52.63
52.6352.64
52.65 52.66 52.68 52.70 52.7252.52 52.55 52.5952.61
52.61
52.6252.60
52.63
52.6452.60 52.66 52.7152.67 52.73 52.74 52.7652.57
T: FTMS + p ESI Full ms [350.00-615.00]
460.0 460.2 460.4 460.6 460.8 461.0 461.2 461.4 4m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
460.4938
460.7391
460.9855
461.2343
461.4847
460.2342459.9875
Peptide Name Conc (nM)
Bid BH3
1 5 10 100 1000Avg. -- 0.00039 0.00097 0.01210 0.11674
Std Dev -- 7.1E-05 0.000163 0.002023 0.012911
%CV 18.11 16.75 16.72451 11.05993
z-prime 0.61
Missing ScansBid BH3 +4
Bid BH3 +5
Bid BH3 +4
∆ppm = 2.7 Bid BH3 +5
Each peptide analyzed was interrogated for possible fragmentation prior to LC analysis. Neat solutions of each peptide were individually infused to determine the peptide fragmentation pattern. (Figure 5)
Bid BH3 85-98
Survivin 2B 80-88
Survivin 85-93
Bid BH3
Survivin 85-93
Survivin 80-88
Bid BH3 85-98
Bid BH3
ResultsTheoretical exact mass calculations were confirmed for each peptide by directly infusing with 1 μg/mL solution of each compound at 5 μL/min. (Figure 2) The charge states producing the most abundant signal for each peptide were determined during the infusion procedure and the mass range for the full scan experiment set accordingly to monitor all relevant charge states. Peptide charge states producing a low level response were excluded from the data collection window to reduce overall data file size, with all charge state ions below 10% of the total signal excluded from the collection range. Files containing 96 or more injections were limited to an overall size of less than 500MB.
F: FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
530.8096
680.2656
466.7800
508.2179
623.2443354.2084
779.3337344.8767 374.7192 580.3428
431.2611
290.1454
709.8824254.6124 890.3651789.3177 932.5519
FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
452.7581
588.3163
631.8318776.4509
502.2922904.5093
705.4138
530.8033388.7289
438.7608
948.4990353.2104 677.4188228.1338 1003.5778
876.5143339.2130
793.4769
762.4361
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
943.4174
624.2437
607.2169794.3123
693.2651 907.3964
711.2756523.1965 812.3231777.2831
638.2805
535.2717390.1436306.1443235.1074 506.1700
289.0960 889.3856386.1664881.3821 962.6227
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
200 400 600 800 1000 1200 1400 1600 1800 2000 2200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
943.4185613.6514932.4922
1067.6248 1409.6700 1527.7390 2012.27161737.0157
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
509.5845460.4916
943.4185613.6514 763.8723931.4894272.1717 597.8999 722.3664657.9211 766.9362368.5936
327.5356431.9845
368.2 368.4 368.6 368.8 369.0 369.2 369.4 369.6 369.8 370.0m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
368.5929
368.7933
368.9938
369.1942
369.3950368.1898 368.3896 369.2198 369.5966 369.9756368.8653
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
233.1645
257.1968
422.2392
550.3342
368.7208276.1339 571.3556736.4341
294.1443 443.2971
649.4022325.2048
589.3661
533.3080 719.4057849.5180746.4187
453.2812
896.2707
RT: 31.06 - 32.79 SM: 7B
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
50
100 0
50
1000
50
100
Rel
ativ
e A
bund
ance
0
50
100 NL: 1.26E6m/z= 422.2371-422.2413 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 6.34E5m/z= 624.2406-624.2468 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.83E6m/z= 631.8286-631.8350 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.57E6m/z= 680.2622-680.2690 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
613.6508
680.2655530.8094
508.2194
466.7798
623.2421
374.7191 594.3468 920.4725431.2617 779.3320354.2084
290.1460 763.8685931.4531
911.4638832.9104
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
20
40
60
80
1000 32.0432.0331.20 31.66
32.4631.6632.4531.6531.21 32.47
31.19 32.0532.0231.22 32.0531.65
32.44 32.4831.6831.1832.02
31.6431.22 32.06 32.4332.4931.23 31.69
31.73 32.0731.28 32.5431.63 32.01 32.4331.53 32.532.16
6 High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS
High Throughput Screening in Drug Discovery for Cancer Research Peptides Using High Resolution LCMS Keeley Murphy1; Maciej Bromirski2; Francois A. Espourteille1 ;1 Thermo Fisher Scientific, San Jose , CA; 2 Thermo Fisher Scientific, Bremen, Germany
Conclusion Liquid chromatography with high resolution mass spec analysis provided a robust
and reproducible method for high throughput screening and simultaneous analysis of multiple peptides at multiple charge states over the course of more that 3000 individual sample injections.
Full scan data collection across a wide mass range enabled the acquisition of spectral information for the entire isotopic charge envelope without sacrificing data quality.
Statistical analysis of a large injection set resulted in Z’ values ranging from 0.61 to 0.85 indicating method robustness the analysis.
Multiplexing using a four-LC channel system provided rapid injection cycle times of 30 seconds, on average, while proving separation from detergents and other interferences containing in sample matrixes.
Full Scan / Full Scan AIF data collection allows for simultaneous Full Scan quantitation as well MS/MS confirmation or quantitation with minimal reduction in instrument scan speed.
References1. Zhang,J.-H.; Chung,T.D.Y.; Oldenburg,K.R. J. Biomol. Screening 1999, 4, 67-73.
2. Roddy,T.P.; Horvath,C.R.; Stout,S.J. Anal. Chem. 2007, 79, 8207-8213.
OverviewPurpose: To implement high resolution accurate mass detection for the simultaneous analysis of multiple components in a high throughput screening assay.
Methods: Several peptides commonly monitored for cancer research were analyzed at various concentration levels in HEPES buffer solutions to determine signal response, linearity,-reproducibility, and Z’ value.
Results: Full scan mode at a resolving setting of 70,000 was utilized for the analysis of several thousand sample sets at cycle time of 30 seconds per sample. Four individual peptides were simultaneously analyzed with results demonstrating a linear signal response across the working range of the assay with analyte sensitivity in the low nM range. Full Scan operation at 70,000 resolving power enabled for data collection across a wide mass range allowing for multiple peptide monitoring at multiple charge states and detection of unexpected sample changes with no impact on instrument performance.
IntroductionLead discovery groups are constantly developing new methodologies to screen large chemical libraries against a specific target. The majority of these methods utilize plate reader devices, ELISA, and other analytical techniques that are amenable to high throughput analysis. Existing analytical methodology used for screening can be less than ideal due to sample prep considerations, limit of detection, and specificity of analyte detection. In these cases high resolution LCMS can provide a high quality alternative while maintaining a sampling rate that is suitable for HTS requirements. Liquid chromatography allows for analysis of samples in matrices that otherwise cause interference in the MS source, while high resolution MS provides sensitivity and specificity along with ease of use without compromising data quality. Two commercially available peptide sets commonly targeted for cancer research were analyzed in a simulated enzymatic screening assay experiment. Survivin 2B and Bid BH3 which are often targeted for analysis for their role in cell apoptosis were monitored at various concentrations in a high throughput screening experiment and the results analyzed to determine signal response, linearity,-reproducibility, and Z’ value.
MethodsSample Preparation
Five lyophilized peptides were ordered (catalog numbers: Survivin 2B (80-88) cat# 62693, Survivin (85-93) cat# 62691, Bid-BH3 cat# 61631, Bid BH3 (85-98) cat# 62485 and Substance P cat# 61694 from AnaSpec™, San Jose, CA). Each peptide was reconstituted in a deionized water at 1 mg/mL. Serial dilutions of Survivin and Bid-BH3 were prepared at concentrations of 1 nM, 5 nM, 10nM, 100 nM, and 1000 nM in in a 50 mM HEPES solution containing 50 mM MgCl2, 50mM Citric Acid, Tween20, and 1% (v/v) DMSO). Substance P was then added to each dilution level as an internal standard at a final concentration of 100 nM.
Liquid Chromatography and Multiplexing
Samples were injected onto a C18, 42.1 x 30 mm, 3.5 µm HPLC column. Analyte elution was accomplished using mobile phase A - water + 0.1% Formic Acid (v/v) and mobile phase B - Acetonitrile + 0.1% Formic Acid (v/v) with a 1-minute step gradient at a flow rate of 1.2 mL/min. The step gradient was performed at 0-10 sec, 2% B, 11-35 sec, 35%B, 36-65 sec, 95% B, and 66-100 sec, 5% B. All methods were completed using a Thermo Scientific Transcend LX-4 system with a dual injector arm with DLW (Dynamic Load and Wash). LC multiplexing was implemented with a data window of 18 seconds per LC channel.
Mass Spectrometry
A Thermo Scientific Exactive Plus bench-top Orbitrap mass spectrometer (Figure 1) was used in Full Scan and Full Scan all-ions-fragmentation (AIF). Full Scan data was collected across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz. A maximum inject time of 250ms for the Full Scan was applied. Full Scan AIF was collected with Full Scan across a mass range of 350-615 m/z at resolution 70,000 and a spectral speed of 3 Hz, and Full Scan AIF across a range of 200 – 2000 m/z at resolution of 17,500 and a spectral speed of 12 Hz using a Normalized Collision Energy of 25. A maximum inject time of 250ms was applied for the Full Scan with 50ms applied for the Full Scan AIF.
Ion source conditions were consistent for all MS experiment scan modes with the following parameters held constant, Vaporizer temperature 500°C, capillary temperature 375°C, sheath gas 60, and AUX gas 20. Prior to experimental data collection, the instrument was calibrated in positive ion mode using Pierce LTQ Velos ESI Positive Ion Calibration Solution.
FIGURE 1. Exactive Plus Instrument Schematic
AnaSpec is a trademark of AnaSpec, Inc. Gubbs is a trademark of Gubbs, Inc. Microsoft and Excel are registered trademarks of Microsoft Corporation. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others.
Sample sets were also collected using All Ion Fragment (AIF) to collect fragmentation spectra for all peptides present in the sample injection. The Full Scan was collected at a resolving power of 70,000 at 200m/z while the AIF was collected at a resolving power of 17,500 at 200m/z. The scans at the resolving power specified above allow for an average of 30 scans across the six second wide chromatographic peak. (Figure 4)
Samples in HEPES Buffer solution were analyzed at 5 concentration points ranging from 1nM to 1000nM with 288 replicate injections at each concentration level. The average peak area ratio was used to calculate %CV at each concentration and generate a calibration curve. (Table 1) The LOQ was determined to be 1nM for three peptides and 5nM for the fourth, with a linear signal response across the detected concentration range. Three of the peptides demonstrated a linear and reproducible response with %CVs below 20% at all concentration levels. The fourth peptide, although detectable at all concentration points displayed %CVs above 20% even at increasing concentration levels. Z-prime statistical analysis provides an indication of overall assay robustness based on the average and standard deviation of a positive and negative control. Z-prime values above 0.5 indicate a robust and acceptable assay. The z-prime for the forth peptide was well below 0.5 with a value of 0.32, indicating a lack of robustness in the analysis. Upon subsequent examination an unresolved interference was observed for the m/z of the fourth peptide that was not present during assay method development. The m/z collection range utilized in the full scan MS experiment allowed for reanalysis of the peptide at an alternate charge that provided an acceptable but lower signal response. The average, standard deviation, %CV, and z-prime was recalculated for the fourth peptide at the alternate charge state through re-interrogation of the previously collect data. (Figure 3)
In all runs, multiple sample injections were collected into a single data file format using Thermo Scientific Xcalibur and Aria software to automatically control data acquisition start and stop times for each sample set. Commercially available peptides were analyzed at various concentration levels and over multiple replicates to determine the coefficient of variation, linear response, and lower limit of quantitation. Results for each experiment type were compared for overall performance and ease of use.
Data Analysis SoftwareThermo Scientific Pinpoint software was used for exact mass calculation of all peptides at each of the observable charge states. Exact mass information was saved in Microsoft® Excel® for later use. Thermo Scientific QuickCalc software (powered by Gubbs Inc., GMSU Gubbs™ Mass Spec Utilities, Atlanta, GA) was used for all chromatographic data review, and report generation. Compound information was imported into QuickCalc™ software using an Excel import template containing the required m/z information. The compound information was stored in QuickCalc software for later use. The compound information was then grouped into a “compound set” and saved, allowing the exact m/z information for multiple compounds to be easily recalled and applied to an entire data set for easy chromatographic review. QuickCalc software was also used to automatically extract and sort each of the 96 injections contained in a data file and then display individual chromatographic peaks in a table view correlated with all sample information related to each individual injection.
Figure 5. Infusion of neat peptide solutions at 10uM conc. and resulting MSMS spectra
The fragmentation data collected during infusion was used to analyze AIF data collected during Full Scan analysis. The most intense fragmentations for each peptide were used to generate extracted ion chromatograms for the AIF data. The results demonstrate the presence of the expected fragmentation patterns for all peptides with scan speed, peak shape, retention time, and sensitivity adequate for MSMS confirmation as well accurate quantitation. The addition of the AIF did not affect the quantitative results of the Full Scan component of the experiment due to the rapid scanning speed of the MS.
FIGURE 4. AIF collection at 17,500 from 200-1000m/z. Scan settings provide for an average of 30 scans across the 6 second peak.
FIGURE 6. MSMS extracted ion chromatograms (XIC) for all four peptide in simultaneous analysis across a four channel multiplexing system. (Top) AIF XIC’s for each individual peptide across a four channel system. (Bottom) AIF spectra at chromatographic peak apex.
FIGURE 2. Top: Full scan peptide mix from 200 to 2000m/z. Bottom: zoomed scan range from 200 to 950m/z.
Full Scan data collection window
**Interference
Peptide Name Conc (nM)
Survivin 85-93
1 5 10 100 1000Avg. 0.012532 0.063424 0.135694 1.435063 12.96369
Std Dev 0.001733 0.007772 0.011968 0.16085 0.562784%CV 13.82914 12.25476 8.820187 11.20856 4.34123
z-prime 0.87
Survivin 2B 80-88
1 5 10 100 1000Avg. -- 0.005237 0.01118 0.133545 1.28023
Std Dev -- 0.000832 0.001688 0.019558 0.126222%CV -- 15.87972 15.0943 14.64532 9.859341
z-prime 0.71
Bid BH3 85-98
1 5 10 100 1000Avg. 0.00490 0.02708 0.05928 0.78428 7.52874
Std Dev 0.00094 0.004446 0.007849 0.097311 0.380001%CV 19.18882 16.41506 13.24001 12.4077 5.047339
z-prime 0.81
Bid BH3
1 5 10 100 1000Avg. 0.01718 0.04581 0.08430 0.62186 5.64208
Std Dev 0.003777 0.007009 0.01349 0.20801 2.483671%CV 21.98924 15.30206 16.00155 33.44948 44.0205
z-prime 0.32
Table 1. Mean, standard deviation, %CV and z-prime for each peptide analyzed. Highlighted values indicate %CV and z-prime values above acceptable levels.
FIGURE 3. Reanalysis of Bid BH3. (Top Left) Bid BH3 scans at +4 and +5, missing scans indicate deviation outside of 5ppm analysis window. (Top Right) MS spectra at +4, ∆ppm = 7.1 indicate an unresolved interference. (Bottom Left) MS spectra at +5, ∆ppm = 2.7. (Bottom Right) Table of recalculated Avg, Std. Dev., %CV, and z-prime.
52.55 52.60 52.65 52.70 52.75Time (min)
0
20
40
60
80
1000
20
40
60
80
100
Rel
ativ
e A
bund
ance
52.62
52.63
52.6352.64
52.65 52.66 52.68 52.70 52.7252.52 52.55 52.5952.61
52.61
52.6252.60
52.63
52.6452.60 52.66 52.7152.67 52.73 52.74 52.7652.57
T: FTMS + p ESI Full ms [350.00-615.00]
460.0 460.2 460.4 460.6 460.8 461.0 461.2 461.4 4m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
460.4938
460.7391
460.9855
461.2343
461.4847
460.2342459.9875
Peptide Name Conc (nM)
Bid BH3
1 5 10 100 1000Avg. -- 0.00039 0.00097 0.01210 0.11674
Std Dev -- 7.1E-05 0.000163 0.002023 0.012911
%CV 18.11 16.75 16.72451 11.05993
z-prime 0.61
Missing ScansBid BH3 +4
Bid BH3 +5
Bid BH3 +4
∆ppm = 2.7 Bid BH3 +5
Each peptide analyzed was interrogated for possible fragmentation prior to LC analysis. Neat solutions of each peptide were individually infused to determine the peptide fragmentation pattern. (Figure 5)
Bid BH3 85-98
Survivin 2B 80-88
Survivin 85-93
Bid BH3
Survivin 85-93
Survivin 80-88
Bid BH3 85-98
Bid BH3
ResultsTheoretical exact mass calculations were confirmed for each peptide by directly infusing with 1 μg/mL solution of each compound at 5 μL/min. (Figure 2) The charge states producing the most abundant signal for each peptide were determined during the infusion procedure and the mass range for the full scan experiment set accordingly to monitor all relevant charge states. Peptide charge states producing a low level response were excluded from the data collection window to reduce overall data file size, with all charge state ions below 10% of the total signal excluded from the collection range. Files containing 96 or more injections were limited to an overall size of less than 500MB.
F: FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
530.8096
680.2656
466.7800
508.2179
623.2443354.2084
779.3337344.8767 374.7192 580.3428
431.2611
290.1454
709.8824254.6124 890.3651789.3177 932.5519
FTMS + p ESI Full ms2 [email protected] [150.00-2000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
452.7581
588.3163
631.8318776.4509
502.2922904.5093
705.4138
530.8033388.7289
438.7608
948.4990353.2104 677.4188228.1338 1003.5778
876.5143339.2130
793.4769
762.4361
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
943.4174
624.2437
607.2169794.3123
693.2651 907.3964
711.2756523.1965 812.3231777.2831
638.2805
535.2717390.1436306.1443235.1074 506.1700
289.0960 889.3856386.1664881.3821 962.6227
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
200 400 600 800 1000 1200 1400 1600 1800 2000 2200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
943.4185613.6514932.4922
1067.6248 1409.6700 1527.7390 2012.27161737.0157
Peptide_Infusion_10ug-mLT: FTMS + p ESI Full ms [200.00-2200.00]
300 400 500 600 700 800 900m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
251.1608466.2482
534.3162
356.5467
509.5845460.4916
943.4185613.6514 763.8723931.4894272.1717 597.8999 722.3664657.9211 766.9362368.5936
327.5356431.9845
368.2 368.4 368.6 368.8 369.0 369.2 369.4 369.6 369.8 370.0m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
368.5929
368.7933
368.9938
369.1942
369.3950368.1898 368.3896 369.2198 369.5966 369.9756368.8653
FTMS + p ESI Full ms2 [email protected] [66.70-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
233.1645
257.1968
422.2392
550.3342
368.7208276.1339 571.3556736.4341
294.1443 443.2971
649.4022325.2048
589.3661
533.3080 719.4057849.5180746.4187
453.2812
896.2707
RT: 31.06 - 32.79 SM: 7B
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
50
100 0
50
1000
50
100
Rel
ativ
e A
bund
ance
0
50
100 NL: 1.26E6m/z= 422.2371-422.2413 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 6.34E5m/z= 624.2406-624.2468 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.83E6m/z= 631.8286-631.8350 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
NL: 5.57E6m/z= 680.2622-680.2690 F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00] MS Curve_Plate_Run_7_253
F: FTMS + p ESI Full ms2 [email protected] [200.00-1000.00]
200 300 400 500 600 700 800 900 1000m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
613.6508
680.2655530.8094
508.2194
466.7798
623.2421
374.7191 594.3468 920.4725431.2617 779.3320354.2084
290.1460 763.8685931.4531
911.4638832.9104
31.2 31.4 31.6 31.8 32.0 32.2 32.4 32.6Time (min)
0
20
40
60
80
1000 32.0432.0331.20 31.66
32.4631.6632.4531.6531.21 32.47
31.19 32.0532.0231.22 32.0531.65
32.44 32.4831.6831.1832.02
31.6431.22 32.06 32.4332.4931.23 31.69
31.73 32.0731.28 32.5431.63 32.01 32.4331.53 32.532.16
Thermo Fisher Scientific, San Jose, CA USA is ISO Certified.
PN63621_E 06/12S
Africa-Other +27 11 570 1840Australia +61 3 9757 4300Austria +43 1 333 50 34 0Belgium +32 53 73 42 41Canada +1 800 530 8447China +86 10 8419 3588Denmark +45 70 23 62 60
Europe-Other +43 1 333 50 34 0Finland/Norway/Sweden +46 8 556 468 00France +33 1 60 92 48 00Germany +49 6103 408 1014India +91 22 6742 9434Italy +39 02 950 591
Japan +81 45 453 9100Latin America +1 561 688 8700Middle East +43 1 333 50 34 0Netherlands +31 76 579 55 55New Zealand +64 9 980 6700Russia/CIS +43 1 333 50 34 0South Africa +27 11 570 1840
Spain +34 914 845 965Switzerland +41 61 716 77 00UK +44 1442 233555USA +1 800 532 4752
www.thermoscientific.com©2012 Thermo Fisher Scientific Inc. All rights reserved. ISO is a trademark of the International Standards Organization. All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries. This information is presented as an example of the capabilities of Thermo Fisher Scientific Inc. products. It is not intended to encourage use of these products in any manners that might infringe the intellectual property rights of others. Specifications, terms and pricing are subject to change. Not all products are available in all countries. Please consult your local sales representative for details.
