Summary of Study ST003729
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002315. The data can be accessed directly via it's Project DOI: 10.21228/M8D26K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)
| Study ID | ST003729 |
| Study Title | Honey bee egg composition changes seasonally and after acute maternal virus infection. |
| Study Type | Metabolomics and lipidomics |
| Study Summary | Honey bee (Apis mellifera) colonies depend on the reproductive output of their queens, which in turn is contingent on the care provided by worker bees. In this study, we collected eggs from honey bee queens in natural field conditions and found that egg collection date strongly influenced egg composition, likely reflecting seasonal variations in pollen resources. These findings highlight that while viral infections can induce transgenerational effects on egg proteomes under short-term experimental conditions, such effects are less apparent in natural settings and can be overshadowed by seasonal and other ecological factors. |
| Institute | University of British Columbia |
| Department | Biochemistry and Molecular Biology, Life Sciences Institute |
| Laboratory | Foster Lab |
| Last Name | Alcazar Magana |
| First Name | Armando |
| Address | 2350 Health Sciences Mall |
| armando.alcazarmagana@ubc.ca | |
| Phone | 5416097172 |
| Submit Date | 2024-09-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-03-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002315 |
| Project DOI: | doi: 10.21228/M8D26K |
| Project Title: | Honey bee egg composition changes seasonally |
| Project Summary: | Here we investigate bee eggs sampled from a field survey to see if the lipid and metabolite composition differs as a result of naturally-occurring queen virus infections. |
| Institute: | University of British Columbia |
| Department: | Biochemistry and Molecular Biology, Life Sciences Institute |
| Laboratory: | Foster Lab |
| Last Name: | Alcazar Magana |
| First Name: | Armando |
| Address: | 2350 Health Sciences Mall, Vancouver, BC, V6T1Z3, Canada |
| Email: | armando.alcazarmagana@ubc.ca |
| Phone: | 5416097172 |
Subject:
| Subject ID: | SU003861 |
| Subject Type: | Insect |
| Subject Species: | Apis mellifera |
| Taxonomy ID: | 7460 |
| Gender: | Not applicable |
Factors:
Subject type: Insect; Subject species: Apis mellifera (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA407290 | 28 | honey bee egg | Beekeeper1-Jun15 |
| SA407291 | 33 | honey bee egg | Beekeeper1-Jun15 |
| SA407292 | 32 | honey bee egg | Beekeeper1-Jun15 |
| SA407293 | 31 | honey bee egg | Beekeeper1-Jun15 |
| SA407294 | 30 | honey bee egg | Beekeeper1-Jun15 |
| SA407295 | 29 | honey bee egg | Beekeeper1-Jun15 |
| SA407296 | 2 | honey bee egg | Beekeeper1-May14 |
| SA407297 | 1 | honey bee egg | Beekeeper1-May14 |
| SA407298 | 10 | honey bee egg | Beekeeper1-May14 |
| SA407299 | 9 | honey bee egg | Beekeeper1-May14 |
| SA407300 | 3 | honey bee egg | Beekeeper1-May14 |
| SA407301 | 4 | honey bee egg | Beekeeper1-May14 |
| SA407302 | 5 | honey bee egg | Beekeeper1-May14 |
| SA407303 | 6 | honey bee egg | Beekeeper1-May14 |
| SA407304 | 7 | honey bee egg | Beekeeper1-May14 |
| SA407305 | 8 | honey bee egg | Beekeeper1-May14 |
| SA407306 | 39 | honey bee egg | Beekeeper2-Jun16 |
| SA407307 | 40 | honey bee egg | Beekeeper2-Jun16 |
| SA407308 | 37 | honey bee egg | Beekeeper2-Jun16 |
| SA407309 | 41 | honey bee egg | Beekeeper2-Jun16 |
| SA407310 | 42 | honey bee egg | Beekeeper2-Jun16 |
| SA407311 | 43 | honey bee egg | Beekeeper2-Jun16 |
| SA407312 | 45 | honey bee egg | Beekeeper2-Jun16 |
| SA407313 | 46 | honey bee egg | Beekeeper2-Jun16 |
| SA407314 | 47 | honey bee egg | Beekeeper2-Jun16 |
| SA407315 | 38 | honey bee egg | Beekeeper2-Jun16 |
| SA407316 | 44 | honey bee egg | Beekeeper2-Jun16 |
| SA407317 | 36 | honey bee egg | Beekeeper2-Jun16 |
| SA407318 | 34 | honey bee egg | Beekeeper2-Jun16 |
| SA407319 | 35 | honey bee egg | Beekeeper2-Jun16 |
| SA407320 | 17 | honey bee egg | Beekeeper2-May15 |
| SA407321 | 11 | honey bee egg | Beekeeper2-May15 |
| SA407322 | 12 | honey bee egg | Beekeeper2-May15 |
| SA407323 | 15 | honey bee egg | Beekeeper2-May15 |
| SA407324 | 13 | honey bee egg | Beekeeper2-May15 |
| SA407325 | 19 | honey bee egg | Beekeeper2-May15 |
| SA407326 | 18 | honey bee egg | Beekeeper2-May15 |
| SA407327 | 20 | honey bee egg | Beekeeper2-May15 |
| SA407328 | 21 | honey bee egg | Beekeeper2-May15 |
| SA407329 | 75 | honey bee egg | Beekeeper3-Jun27 |
| SA407330 | 83 | honey bee egg | Beekeeper3-Jun27 |
| SA407331 | 76 | honey bee egg | Beekeeper3-Jun27 |
| SA407332 | 77 | honey bee egg | Beekeeper3-Jun27 |
| SA407333 | 78 | honey bee egg | Beekeeper3-Jun27 |
| SA407334 | 79 | honey bee egg | Beekeeper3-Jun27 |
| SA407335 | 80 | honey bee egg | Beekeeper3-Jun27 |
| SA407336 | 81 | honey bee egg | Beekeeper3-Jun27 |
| SA407337 | 82 | honey bee egg | Beekeeper3-Jun27 |
| SA407338 | 89 | honey bee egg | Beekeeper3-Jun27 |
| SA407339 | 84 | honey bee egg | Beekeeper3-Jun27 |
| SA407340 | 85 | honey bee egg | Beekeeper3-Jun27 |
| SA407341 | 86 | honey bee egg | Beekeeper3-Jun27 |
| SA407342 | 87 | honey bee egg | Beekeeper3-Jun27 |
| SA407343 | 88 | honey bee egg | Beekeeper3-Jun27 |
| SA407344 | 90 | honey bee egg | Beekeeper3-Jun27 |
| SA407345 | 92 | honey bee egg | Beekeeper3-Jun27 |
| SA407346 | 93 | honey bee egg | Beekeeper3-Jun27 |
| SA407347 | 94 | honey bee egg | Beekeeper3-Jun27 |
| SA407348 | 73 | honey bee egg | Beekeeper3-Jun27 |
| SA407349 | 74 | honey bee egg | Beekeeper3-Jun27 |
| SA407350 | 56 | honey bee egg | Beekeeper3-Jun27 |
| SA407351 | 72 | honey bee egg | Beekeeper3-Jun27 |
| SA407352 | 59 | honey bee egg | Beekeeper3-Jun27 |
| SA407353 | 48 | honey bee egg | Beekeeper3-Jun27 |
| SA407354 | 49 | honey bee egg | Beekeeper3-Jun27 |
| SA407355 | 50 | honey bee egg | Beekeeper3-Jun27 |
| SA407356 | 52 | honey bee egg | Beekeeper3-Jun27 |
| SA407357 | 53 | honey bee egg | Beekeeper3-Jun27 |
| SA407358 | 54 | honey bee egg | Beekeeper3-Jun27 |
| SA407359 | 55 | honey bee egg | Beekeeper3-Jun27 |
| SA407360 | 57 | honey bee egg | Beekeeper3-Jun27 |
| SA407361 | 58 | honey bee egg | Beekeeper3-Jun27 |
| SA407362 | 60 | honey bee egg | Beekeeper3-Jun27 |
| SA407363 | 71 | honey bee egg | Beekeeper3-Jun27 |
| SA407364 | 61 | honey bee egg | Beekeeper3-Jun27 |
| SA407365 | 62 | honey bee egg | Beekeeper3-Jun27 |
| SA407366 | 63 | honey bee egg | Beekeeper3-Jun27 |
| SA407367 | 64 | honey bee egg | Beekeeper3-Jun27 |
| SA407368 | 65 | honey bee egg | Beekeeper3-Jun27 |
| SA407369 | 66 | honey bee egg | Beekeeper3-Jun27 |
| SA407370 | 67 | honey bee egg | Beekeeper3-Jun27 |
| SA407371 | 68 | honey bee egg | Beekeeper3-Jun27 |
| SA407372 | 69 | honey bee egg | Beekeeper3-Jun27 |
| SA407373 | 51 | honey bee egg | Beekeeper3-Jun27 |
| Showing results 1 to 84 of 84 |
Collection:
| Collection ID: | CO003854 |
| Collection Summary: | Honey bee queens and their eggs were sampled from colonies in the field in 2021. Samples were collected twice from the two British Columbia beekeepers (in Grand Forks and Vernon), first on May 14 & 15 and then again on June 15 & 16, and collected from a Lethbridge, Alberta, beekeeper on June 27 & 28. At each time point, 10 eggs still standing on end (not fallen onto their side, which is indicative of older eggs close to hatching) were collected using a Chinese grafting tool and transferred to Eppendorf tubes. All samples were collected directly onto dry-ice and subsequently stored at -70 °C until processing. |
| Sample Type: | Eggs |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003870 |
| Treatment Summary: | No treatment (collection time is of interest and no treatment was administered) |
Sample Preparation:
| Sampleprep ID: | SP003867 |
| Sampleprep Summary: | Eppendorf tubes containing 10 eggs each were centrifuged for 1 min at 14,000 rcf immediately upon removal from the freezer freezer followed by a two-phase extraction protocol adapted from Matyash et al. (2008) with some modifications. Briefly, 100 μL of methanol extraction solvent (75% methanol:water, made with 0.01% BHT-methanol and containing standards of methionine-d3, caffeine-13C3, and ferulic acid-d3 each at 1 ppm and SPLASH LIPIDOMIX (Avanti Polar Lipids, Alabama, USA) at 5 ppm) was added. The eggs were then ground with a mini-pestle to lyse the eggs. The tubes were thoroughly vortexed, and samples were transferred to a 2 mL screw cap tube homogenizer tube. Another 100 μL of extraction solvent was used to rinse the original tube and was also transferred to the homogenization tube to increase yields. 2 ceramic beads were then added and samples were homogenized three times for 30 seconds at 6500 rpm as described for proteomics sample processing. 500 μL of methyl tert-butyl ether was then added and samples were incubated for 1 hour at room temperature while shaking at 1000 rpm. The mixture was transferred to a new tube and centrifuged at 14,000 rcf for 10 min. 600 μL was transferred to a new tube to which 107 μL of water was added (to a final additional concentration of 15%) before incubating again at room temperature for 10 minutes while shaking at 700 rpm. The samples were then centrifuged for 15 min at 14000 rcf at 4C. 300 μL of the upper fraction containing the non-polar (lipid) compounds were transferred to a new tube, while 400 μL of the lower fraction containing the polar (metabolite) compounds were transferred to a different tube. The polar fraction was dried (SpeedVac, Eppendorf) immediately and stored at -70 °C until mass spectrometry analysis. The non-polar fraction was stored in solution at -70 °C and dried immediately before analysis to prevent oxidation. |
| Processing Storage Conditions: | On ice |
Combined analysis:
| Analysis ID | AN006117 | AN006118 | AN006119 |
|---|---|---|---|
| Analysis type | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish | Elute LC |
| Column | GL Sciences Inertsil Ph-3 UHPLC (150 x 2.1mm, 2um) | GL Sciences Inertsil Ph-3 UHPLC (150 x 2.1mm, 2um) | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF |
| MS instrument name | Bruker Impact II | Bruker Impact II | Bruker Impact II |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE |
| Units | Relative Abundance | Relative Abundance | Relative Abundance |
Chromatography:
| Chromatography ID: | CH004646 |
| Chromatography Summary: | Metabolomics with Inertsil Ph-3 UHPLC column (2 µm, 150 x 2.1 mm, GL Sciences) |
| Instrument Name: | Thermo Vanquish |
| Column Name: | GL Sciences Inertsil Ph-3 UHPLC (150 x 2.1mm, 2um) |
| Column Temperature: | 55 |
| Flow Gradient: | 0 min (5% B), 0–1 min (5% B), 1–8 min (35% B), 8–10.5 min (99% B), 10.5–14 min (99% B), 14–14.5 min (5% B), and 14.5–18 min (5% B) |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium acetate; 5 µM medronic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004647 |
| Chromatography Summary: | Lipidomics with Acquity CSH column |
| Instrument Name: | Elute LC |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | 0 min 15% B; 0–2 min 30% B; 2–2.5 min 50% B; 2.5–12 min 80% B; 12–12.5 min 99% B; 12.5–13.5 min 99% B; 13.5–13.7 min 15% B; 13.7-17 min 15% B. |
| Flow Rate: | 0.5 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005823 |
| Analysis ID: | AN006117 |
| Instrument Name: | Bruker Impact II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Data-dependent acquisitions were conducted in positive (ESI+) and negative (ESI-) ionization modes. For ESI+, the settings were as follows: a capillary voltage of 4,500 V, nebulizer pressure of 2.0 bar, dry gas flow of 9 L/min, dry gas temperature of 220°C, and a mass scan range of 60–1,300 m/z with a 0.6-second cycle time. Collision energy was 20 V ramped from 100 to 250% in MS/MS scans. ESI- used a capillary voltage of -3,500 V. Internal calibration was performed using sodium formate (10 µL of 10 mM injected at 0–0.15 min) to ensure high mass accuracy. The raw data was processed using Progenesis QI™ software (version V3.0.7600.27622) with METLIN™ plugin (version V1.0.7642.33805, NonLinear Dynamics). This involved peak picking, alignment, deconvolution, normalization, and database searching. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005824 |
| Analysis ID: | AN006118 |
| Instrument Name: | Bruker Impact II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Data-dependent acquisitions were performed in positive ionization mode (ESI+) to obtain precursor and fragment ion information for compound annotation. The mass spectrometer settings were as follows: capillary voltage of 4,500 V, nebulizer gas pressure of 2.0 bar, dry gas flow rate of 9 L/min, dry gas temperature of 220°C, mass scan range of 65–1,700 m/z, spectral acquisition rate of 3 Hz, and cycle time of 0.7 s. Collision energy of 20 V was ramped through each MS/MS scan from 100% to 250%. Calibration was carried out by injecting 10 µL of 10 mM sodium formate at the beginning of each run via the 6-port diverter valve. The raw data was processed using Progenesis QI™ software (version V3.0.7600.27622) with METLIN™ plugin (version V1.0.7642.33805, NonLinear Dynamics). This involved peak picking, alignment, deconvolution, normalization, and database searching. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005825 |
| Analysis ID: | AN006119 |
| Instrument Name: | Bruker Impact II |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Data-dependent acquisitions were performed in positive ionization mode (ESI+) to obtain precursor and fragment ion information for compound annotation. The mass spectrometer settings were as follows: capillary voltage of 4,500 V, nebulizer gas pressure of 2.0 bar, dry gas flow rate of 9 L/min, dry gas temperature of 220°C, mass scan range of 65–1,700 m/z, spectral acquisition rate of 3 Hz, and cycle time of 0.7 s. Collision energy of 20 V was ramped through each MS/MS scan from 100% to 250%. Calibration was carried out by injecting 10 µL of 10 mM sodium formate at the beginning of each run via the 6-port diverter valve. The raw data was processed using Progenesis QI™ software (version V3.0.7600.27622) with METLIN™ plugin (version V1.0.7642.33805, NonLinear Dynamics). This involved peak picking, alignment, deconvolution, normalization, and database searching. |
| Ion Mode: | POSITIVE |
