Higher Resolution LC-MS and MS-MS Analysis of Lipid Extracts Using Benchtop Orbitrap-based Mass Spectrometers and LipidSearch Software David A Peake,1 Yasuto Yokoi, 2 Reiko Kiyonami1 and Yingying Huang1 1 Thermo Fisher Scientific, San Jose, USA; 2Mitsui Knowledge Industry, Tokyo, JAPAN Overview Purpose: Benchmark the performance of a new LC-MS/MS system and determine the effect of full scan MS resolution vs. the number of identified lipids in total lipid extracts. Methods: Lipid extracts were profiled using LC-dd-MS/MS analysis using a novel quadrupole-Orbitrap mass spectrometer operated at mass resolution of 30, 60, 120 and 240K. Results: The data presented here shows that lipidomic profiling at higher full scan MS resolution provides more identified lipids during an LC-MS run. The higher acquisition rate of MS/MS spectra also contributes to significantly more lipids being identified. Introduction Lipids play a key role in cell, tissue and organ physiology with diseases such as cancer and diabetes which involve disruption of their metabolic enzymes and pathways. Identification of unique lipid biomarkers to distinguish healthy humans compared to those with a disease can have an impact on the early detection of diseases and personalized medicine. Because of the complexity of the lipidome, which includes 8 major categories of lipids, over 80 major classes, 300 sub-classes and thousands of lipid species1, HPLC MS/MS methods are often used to separate many overlapping isomeric or isobaric molecular ions in biological samples for increased lipid identification coverage. By employing a high resolution accurate mass (HR/AM) platform equipped with a ultra-high field Orbitrap mass spectrometer (Thermo ScientificTM Q Exactive HFTM MS) to detect lipids after HPLC separation, ultra-high resolution MS and MS/MS analysis provides unambiguous identification of lipids in biological samples. However, it is extremely challenging to process all the MS and MS/MS data manually. A sophisticated software with an extensive database is required to identify all detected lipids HPLC MS/MS data. The newly-released Thermo ScientificTM LipidSearchTM software enables automated identification of lipids from biological samples based on its large lipid database which includes >1.5 million lipid ions and predicted fragment ions. In addition, relative quantification of identified lipid precursors can be carried out in the same LC/MS/MS experiment. In this study, we present that hundreds of lipid species can be simultaneously identified and quantified in a single LC/MS-MS experiment by using optimized HPLC separation and HR/AM MS and data-dependent MS2 conditions. Methods TABLE 1. HPLC Gradient Time, min %A 0.00 68 %B 32 1.50 68 32 4.00 55 45 5.00 48 52 8.00 42 58 11.00 34 66 14.00 30 70 18.00 25 75 21.00 3 97 25.00 3 97 25.01 68 32 33.00 68 32 Data Processin LC-MS/MS Data Processing 1) Peak Detection. Read raw 2) Identification. Candidate m database >106 entries of accu each potential lipid structure a 3) Alignment. The search res window and the results are co 4) Quantification. The accura each identified lipid precursor 5) Statistical Analysis. t-Test sample vs. control groups, and FIGURE 1. LipidSearch Work LC-MS Sample Preparation. Bovine brain, heart, liver and yeast total lipid extracts (2.5 mg/mL in Chloroform) were purchased from Avanti Polar Lipids. Dilution series of each lipid extract was prepared by diluting the stock solutions sequentially into 1.25 µg/µL, 500 ng/µL, 250 ng/µL, 125 ng/µL and 50 ng/µL in 50:50 Methanol and Isopropanol (IPA). HPLC Method. A Thermo Scientific™ Dionex™ UltiMate™ 3000 Rapid Separation LC (RSLC) system performed separations using the gradient conditions shown in Table 12. Mobile phase A was 60:40 Acetonitrile / Water and mobile phase B was 90:10 IPA / Acetonitrile; both A and B contained 10mM ammonium formate and 0.1% formic acid. The column was an Ascentis Express C18 (Supelco, 2.1 x 100mm, 2.7µm) operated at 55°C, flow rate of 260 µL/min and the injection volume was 2 µL. MS Conditions. Thermo Scientific Q Exactive Plus and Q Exactive HF instruments were employed for untargeted lipid profiling experiments using the instrument operating conditions shown in Table 2. Each instrument was operated under optimized conditions providing sufficient scans across the chromatographic peak profile for accurate relative quantification using the HR/AM precursor ion while simultaneously acquiring dd-MS2 spectra for lipid identification. Data Analysis Software. LipidSearch software was used for lipid identification and relative quantification. 2 Highly Sensitive, Robust MS-Based Workflow for Therapeutic Monoclonal Antibody Analysis from Complex Matrices • • • • • HRAM / Nomin Infusion & LC-M ID based on M DB with 106+ li Integration of m W KO / WT = 0.3 p < 0.0053 KO S/MS system and determine the ified lipids in total lipid extracts. MS analysis using a novel mass resolution of 30, 60, 120 profiling at higher full scan MS MS run. The higher acquisition more lipids being identified. gy with diseases such as cancer enzymes and pathways. ealthy humans compared to etection of diseases and es 8 major categories of lipids, of lipid species1, HPLC MS/MS isomeric or isobaric molecular on coverage. By employing a ped with a ultra-high field active HFTM MS) to detect lipids S/MS analysis provides s. MS and MS/MS data manually. required to identify all detected ScientificTM LipidSearchTM biological samples based on its s and predicted fragment ions. ursors can be carried out in the can be simultaneously ent by using optimized HPLC onditions. TABLE 1. HPLC Gradient Time, min %A 0.00 68 32 1.50 68 32 4.00 55 45 5.00 48 52 8.00 42 58 TABLE 2. Orbitrap Operating Conditions %B 11.00 34 66 14.00 30 70 18.00 25 75 21.00 3 97 25.00 3 97 25.01 68 32 33.00 68 32 HESI Source Pos. or Neg. Ion Aux gas 3 MS Resolution 30K, 60K, 120K, 240K MS Resolution 17.5K, 35K, 70K, 140K Spray volt. 4.2 Top15 dd-MS2 R = 35K kV Top20 dd-MS2 R = 30K S-Lens 50 MS2 Isolation width 1 Da MS2 Isolation width 1 Da Cap. Temp. 320°C Stepped NCE – Pos. 25, 30 Neg. 20, 24, 28 Stepped NCE – Pos. 25, 30 Neg. 20, 24, 28 Heater temp. 300°C AGC target 1E+6 MS 1E+5 MS2 AGC target 1E+6 MS 1E+5 MS2 Results Lipid Identification Results from (1.25 µg/µL) was analyzed by LC/M modes, respectively (Figure 2). Lipi data for all common lipid classes us product ions. For each MS2 spectru the lipid precursor ion m/z stored in summarized for the identified lipid s experimental data (Figure 3). The speed advantage of Q Exactive illustrated in Figure 4, compared to higher resolution (120K) the Q Exac FIGURE 2. High Resolution (70,00 Total ion Chromatograms of Bov Positive Ion Data Processing LC-MS/MS Data Processing Workflow using LipidSearch Software (Figure 1). 1) Peak Detection. Read raw files, MSn and precursor ion accurate masses. 2) Identification. Candidate molecular species are identified by searching a large database >106 entries of accurate m/z (lipid precursor and fragment ions) predicted from each potential lipid structure and positive/negative ion adduct. 3) Alignment. The search results for each individual sample are aligned within a time window and the results are combined into a single report. 4) Quantification. The accurate-mass extracted ion chromatograms are integrated for each identified lipid precursor and the peak areas are obtained. 5) Statistical Analysis. t-Tests determine significantly differences between lipids in sample vs. control groups, and results are displayed in a whisker plot. FIGURE 1. LipidSearch Workflow. FIGURE 3. Search Results for m/z 329.2483 PC(18:0_22:5) Peak Detect 283.2640 820.5 Separation LC (RSLC) system own in Table 12. Mobile phase A 90:10 IPA / Acetonitrile; both A ormic acid. The column was an operated at 55°C, flow rate of nd relative quantification. Q Exactive HF Sheath gas 35 Pos. or Neg. Ion 2.5 mg/mL in Chloroform) were ach lipid extract was prepared µL, 500 ng/µL, 250 ng/µL, 125 (IPA). nstruments were employed for ent operating conditions shown zed conditions providing e for accurate relative ultaneously acquiring dd-MS2 Q Exactive Plus 508.3407 Identify • • • • • HRAM / Nominal mass Infusion & LC-MS data ID based on MSn DB with 106+ lipid species Integration of multiple runs KO 500 Align 400 300 WT KO / WT = 0.36 p < 0.0053 FIGURE 4. Increase in the Number Lipid Extract using dd-LCMS2 with Quan QE Plus (top QE HF (top 2 200 100 0 100ng Thermo Scientific Poster Note • PN-64137-ASMS-EN-0614S 3 250ng Orbitrap Operating Conditions Q Exactive Plus 5 Pos. or Neg. Ion MS Resolution 17.5K, 35K, 70K, 140K 2 Top15 dd-MS2 R = 35K Q Exactive HF Pos. or Neg. Ion MS Resolution 30K, 60K, 120K, 240K Top20 dd-MS2 R = 30K MS2 Isolation width 1 Da MS2 Isolation width 1 Da Stepped NCE – Pos. 25, 30 Neg. 20, 24, 28 Stepped NCE – Pos. 25, 30 Neg. 20, 24, 28 AGC target 1E+6 MS 1E+5 MS2 AGC target 1E+6 MS 1E+5 MS2 Results Improved ID and Relative Q Higher MS resolution lipid pr related lipids overlap even u resolution for identification o two Lyso phospholipid speci during analysis at 2.2 minute needed to separate these tw smaller LPE 18:1 peak (m/z is only partially resolved at 2 required for unequivocal iden lipid species is challenging w Lipid Identification Results from LC/dd-MS2 Data. Bovine heart total lipid extract (1.25 µg/µL) was analyzed by LC/MS and dd-MS/MS in positive and negative ion modes, respectively (Figure 2). LipidSearch software was used to search the LC-MS data for all common lipid classes using a mass tolerance of ±5 ppm for precursor and product ions. For each MS2 spectrum matching a predicted fragmentation pattern from the lipid precursor ion m/z stored in the LipidSearch database, search results are summarized for the identified lipid species with m-score indicating the fit to the experimental data (Figure 3). The speed advantage of Q Exactive HF (120K resolution) and TOP20 dd-MS2 is illustrated in Figure 4, compared to Q Exactive Plus (70K) and TOP15 dd-MS2. At the higher resolution (120K) the Q Exactive HF obtains 20% more lipid identifications. The number of lipids identifie results are shown in Table 3 exceed the sum of positive a where lipids are identified in FIGURE 2. High Resolution (70,000) Accurate Mass Positive and Negative Total ion Chromatograms of Bovine Heart Total Lipid Extract. FIGURE 5. Increased Reso PC and PE Lipid Species. R 500ng_pos_15K_30kms2_top15_200_1200_01 Positive Ion SM: 5B Rt = 2.2 min LipidSearch Software (Figure 1). 480.15764 ecursor ion accurate masses. 15K are identified by searching a large ecursor and fragment ions) predicted from ive ion adduct. +2.1 ppm 43K Negative Ion 100 Relative Abundance vidual sample are aligned within a time gle report. d ion chromatograms are integrated for as are obtained. ficantly differences between lipids in ayed in a whisker plot. LPE 18:1 480.15664 C23H47NO7P 80 +0.1 ppm R = 83K 60 40 480.15713 20 0 480.05 FIGURE 3. Search Results for m/z 880.6068, PC(40:5) M+HCO2329.2483 PC(18:0_22:5) 30K 480.15639 R= 480.10 480.15 60K 120K 480.20 480.25 m/z TABLE 3. Comparison of L Bovine Brain, Heart, Liver Bovine Brain Lipid Class Neg Pos Merged CL 283.2640 820.5862 Match Details 508.3407 Identify FIGURE 4. Increase in the Number of Lipid Species Identified in Bovine Heart Lipid Extract using dd-LCMS2 with Q Exactive HF Compared to Q Exactive Plus 500 Align 400 300 QE Plus (top 15) QE HF (top 20) 200 100 0 100ng 250ng 500ng 1000ng 2500ng 4 Highly Sensitive, Robust MS-Based Workflow for Therapeutic Monoclonal Antibody Analysis from Complex Matrices LPC 13 34 40 PC 49 152 242 LPE 14 15 24 PE 88 73 171 LPS PS LPG PG LPI PI PA SM So Cer CerG1 CerG2 ChE ZyE DG TG CoQ Total 6 4 7 35 24 63 8 2 9 19 19 33 34 41 62 2 31 34 2 2 2 4 8 2 2 4 33 5 26 284 2 4 13 5 37 5 35 86 147 552 936 1 1 Improved ID and Relative Quantitation Results Obtained with Q Exactive HF Higher MS resolution lipid profiling translates into improved identification when closely related lipids overlap even under chromatographic conditions. The effect of MS1 resolution for identification of lipid species at the same retention time is illustrated for two Lyso phospholipid species, 18:1 LPE and 16:0p LPC. These two lipids overlap during analysis at 2.2 minutes at m/z in positive ion of 480.3. The mass resolution needed to separate these two lipids is illustrated in Figure 5. At a resolution of 10K, the smaller LPE 18:1 peak (m/z 480.3085) is overlapped by LPC 16:0p (m/z 480.3449) and is only partially resolved at 22K. The 60K setting giving an actual resolution of 42K is required for unequivocal identification of both M+H ions. Thus, identification of minor lipid species is challenging without sufficient mass resolution, leading to fewer ID’s. . Bovine heart total lipid extract S in positive and negative ion e was used to search the LC-MS ance of ±5 ppm for precursor and edicted fragmentation pattern from database, search results are ore indicating the fit to the ution) and TOP20 dd-MS2 is (70K) and TOP15 dd-MS2. At the 20% more lipid identifications. The number of lipids identified in positive and negative ion, and the aligned (merged) results are shown in Table 3. Note that the number of lipid species after alignment may exceed the sum of positive and negative ion species because of the correlation step where lipids are identified in multiple samples and isomers are present at the MS2 level. ss Positive and Negative Lipid Extract. FIGURE 5. Increased Resolution Improves Identification of Overlapping Lyso 03/28/14 03:31:06 PC and PE Lipid Species. Resolution (m/z 200) = 15K, 30K, 60K and 120K 500ng_pos_15K_30kms2_top15_200_1200_01 SM: 5B Rt = 2.2 min 480.34361 15K +2.1 ppm 43K Negative Ion 480.34454 Relative Abundance LPE 18:1 480.15664 C23H47NO7P 80 +0.1 ppm R = 83K 60 40 480.15713 20 0:5) M+HCO2- 480.34458 30K 480.15639 R= 100 0 480.05 480.30710 480.10 480.15 60K 120K 480.20 480.25 m/z 480.30946 2500ng Neutrals Unknown 3 1 10 5 42 17 7 2 11 3 22 1 8 59 100 2 7 50 20 32 100 100 1 1 19 2 1 5 13 4 45 6. Composition of Lipid 480.30854 480.30 480.35 480.40 480.45 TABLE 3. Comparison of Lipid Species Identified in Total Lipid Extracts of Bovine Brain, Heart, Liver and from Yeast CL 1000ng Brain Heart Liver Yeas Total Bovine Brain Bovine Heart Bovine Liver Yeast Lipid Class Neg Pos Merged Neg Pos Merged Neg Pos Merged Neg Pos Merged s Identified in Bovine Heart Compared to Q Exactive Plus Wt % PA LPC PC LPE PE PG LPI PI PS CL Chol NL: 2.58E5 500ng_pos_15K_30kms2_top15_200_12 FIGURE 00_01#1162-1333 +3.6 ppm RT: 2.13-2.43 AV: 35 T: FTMS + p ESI Full ms R = 10K [250.00-1200.00] NL: 2.43E5 500ng_pos30k_30kms2_top15_200_120 0_01#1087-1253 -2.6 ppm RT: 2.01-2.29 AV: 28 T: FTMS p ESI Full ms R = +22K [250.00-1200.00] NL: 2.97E5 500ng_pos60k_30kms2_top15_200_120 LPC 16:0p 0_01#1100-1263 C24H51NO6P RT: 2.14-2.42 AV: 25 T: FTMS + p ESI Full ms -0.6 ppm [250.00-1200.00] R = 86K NL: 2.82E5 500ng_pos120k_30kms2_top15_200_12 00_01#999-1144 RT: 2.14-2.43 AV: 18 T: FTMS + p ESI Full ms [250.00-1200.00] 480.34658 480.15764 TABLE 4. Typical Composition o Total Lipid Extracts (Avanti Lipid LPC 9 1 2 2 13 34 40 14 28 30 18 36 39 13 25 40 PC 49 152 242 78 141 253 61 137 294 26 58 92 LPE 14 15 24 14 8 17 15 10 17 9 9 12 PE 88 73 171 92 45 165 74 51 248 19 19 34 1 1 7 1 LPS PS LPG PG LPI PI PA SM So Cer CerG1 CerG2 ChE ZyE DG TG CoQ Total 9 6 4 7 35 24 63 37 8 2 9 19 19 34 41 2 2 4 8 2 53 23 26 4 35 33 31 25 62 37 31 34 1 2 2 2 4 33 5 26 284 2 6 2 4 13 5 37 5 3 147 552 936 1 Higher resolution and speed identification and relative qu 3 1 At least 20% more lipid ID’s Orbitrap. LipidSearch provides autom single LC-ddMS2 experimen lipid species. 24 6 38 17 5 48 10 3 10 55 34 33 98 27 41 55 39 56 37 39 91 6 7 12 17 18 5 41 46 3 3 1 2 1 32 351 Four different total lipid extra lipidomics experiments, sepa 65 4 5 3 2 1 5 9 5 3 5 9 5 35 3 45 174 329 528 1087 5 5 29 310 5 9 11 5 9 5 44 1 4 9 2 3 3 2 2 4 27 5 18 1. LIPID MAPS comprehensiv Lipid Res. 2009, 50, S9-S1 3 2. Lipidomics profiling by high dissociation fragmentation: cardiolipins and monolysoc 940–949. dx.doi.org/10.102 2 2 31 248 161 241 568 1297 153 374 607 3 4 References 3 155 3 Conclusion 1 5 86 1 4 7 2 3 Lipid Search is a registered trademark of MKI All other trademarks are the property of Therm This information is not intended to encourage intellectual property rights of others. Thermo Scientific Poster Note • PN-64137-ASMS-EN-0614S 5 Obtained with Q Exactive HF mproved identification when closely conditions. The effect of MS1 me retention time is illustrated for p LPC. These two lipids overlap of 480.3. The mass resolution Figure 5. At a resolution of 10K, the ed by LPC 16:0p (m/z 480.3449) and ving an actual resolution of 42K is ions. Thus, identification of minor resolution, leading to fewer ID’s. tive ion, and the aligned (merged) of lipid species after alignment may s because of the correlation step somers are present at the MS2 level. tification of Overlapping Lyso = 15K, 30K, 60K and 120K TABLE 4. Typical Composition of Total Lipid Extracts (Avanti Lipids) Wt % Brain Heart Liver Yeast PA LPC PC LPE PE PG LPI PI PS CL Chol Neutrals Unknown Total NL: 2.58E5 500ng_pos_15K_30kms2_top15_200_12 FIGURE 00_01#1162-1333 +3.6 ppm RT: 2.13-2.43 AV: 35 T: FTMS + p ESI Full ms R = 10K [250.00-1200.00] NL: 2.43E5 500ng_pos30k_30kms2_top15_200_120 0_01#1087-1253 -2.6 ppm RT: 2.01-2.29 AV: 28 T: FTMS p ESI Full ms R = +22K [250.00-1200.00] NL: 2.97E5 500ng_pos60k_30kms2_top15_200_120 LPC 16:0p 0_01#1100-1263 C24H51NO6P RT: 2.14-2.42 AV: 25 T: FTMS + p ESI Full ms -0.6 ppm [250.00-1200.00] R = 86K NL: 2.82E5 500ng_pos120k_30kms2_top15_200_12 00_01#999-1144 RT: 2.14-2.43 AV: 18 T: FTMS + p ESI Full ms [250.00-1200.00] 3 1 10 5 42 17 7 2 11 3 22 1 8 59 100 2 7 50 20 32 100 100 1 1 19 2 1 5 13 4 45 Composition of Total Lipid Extracts Composition information for the total lipid extracts listed on Avanti Polar Lipids website are shown in Table 4. The LC-MS2 results for each lipid extract injected in duplicate were searched using LipidSearch, and positive and negative ion data were aligned within a 0.4 min window (Table 3). The peak areas for each lipid class were summed and the relative amounts of each lipid class were plotted as % Area from the full scan MS (Figure 6). As expected from the 50 wt % of neutral lipids, the bovine heart extract contained the highest amount of TG (65% by peak area), and the yeast extract contained 61% TG. Brain, liver and yeast extracts contained the most PC. 6. Composition of Lipid Extracts by LC-HRMS Peak Area (%) Brain Liver Yeast Heart 70 60 50 40 30 20 10 Bovine Liver Yeast eg Pos Merged Neg Pos Merged 1 2 2 2 Four different total lipid extracts were profiled and are suitable for benchmarking lipidomics experiments, separation conditions and instrumental optimization. Higher resolution and speed of Q Exactive HF provides more confident identification and relative quantification in a single positive and negative ion run. 3 1 At least 20% more lipid ID’s were obtained using a ultra-high field benchtop Orbitrap. LipidSearch provides automated identification of more than 500 lipid species in a single LC-ddMS2 experiment, and alignment of multiple samples gives over 1000 lipid species. 36 39 13 25 40 61 137 294 26 58 92 15 10 17 9 9 12 74 51 248 19 19 34 7 1 7 3 1 65 24 6 38 17 5 48 10 3 10 34 33 98 27 41 55 37 39 91 6 7 12 5 41 46 3 3 5 9 5 10 3 5 9 5 29 5 9 11 5 9 5 44 1 4 9 2 3 3 2 2 4 27 5 18 1. LIPID MAPS comprehensive classification system for lipids. E Fahy et al., J. Lipid Res. 2009, 50, S9-S14. doi: 10.1194/jlr.R800095-JLR200. 3 2. Lipidomics profiling by high-resolution LC-MS and high-energy collisional dissociation fragmentation: focus on characterization of mitochondrial cardiolipins and monolysocardiolipins. S Bird, et al., Anal. Chem. 2011, 83, 940–949. dx.doi.org/10.1021/ac102598u. 2 2 31 248 161 241 568 1297 153 374 607 3 4 References 3 155 3 Conclusion 18 23 Heart Yeast d in Total Lipid Extracts of Brain 0 480.45 Liver 480.40 3 Lipid Search is a registered trademark of MKI and Ascentis Express is a registered trademark of Sigma-Aldrich. 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. PO64137-EN 0614S 6 Highly Sensitive, Robust MS-Based Workflow for Therapeutic Monoclonal Antibody Analysis from Complex Matrices www.thermoscientific.com ©2014 Thermo Fisher Scientific Inc. All rights reserved. ISO is a trademark of the International Standards Organization. Lipid Search is a registered trademark of MKI and Ascentis Express is a registered trademark of Sigma-Aldrich. 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