Mass Spectral (MS) and Retention Time Index (RI) Libraries of GC-MS Metabolite Profiles

 

Library overview:

T_MSRI_ID.txt (version 01.03.2004; version 02):

            Annotated GC-TOF-MS spectra   

Q_MSRI_ID.txt (version 01.03.2004):

            Annotated quadrupole GC-MS spectra               

 

T_MSRI_NS.txt (version 01.03.2004 ):

            Non-supervised collection of GC-TOF-MS spectra

            of plant species

Q_LJA_NS.txt (version 01.03.2004):

            Non-supervised collection of quadrupole GC-MS spectra

            of Lotus japonicus (Regel) K. Larsen

Q_LYC_NS.txt (version 01.03.2004):

            Non-supervised collection of quadrupole GC-MS spectra

            of Lycopersicon esculentum Mill. and related wild species

 

Library description (T_MSRI_ID, Q_MSRI_ID):

T_MSRI_ID.xls (version 01.03.2004)

 

 

Methods:

M[1] (EITTMS):

Sampling:                         shock freezing in liquid nitrogen

Extraction:                       hot (70°C) methanol/ water/ chloroform (approx. 4:1:2; v/v/v)

Fractionation:                   polar metabolites

liquid partitioning into methanol/water (approx. 1:1; v/v), and chloroform (chloroform phase is discarded).

Derivatization:                   =N-O-CH3  (methoxyamine hydrochloride/ pyridine reagent, 20 mg / ml)

                                       -Si(CH3)3  (N-methyl-N-(trimethylsilyl)-trifluoroacetamide, MSTFA reagent)

RI system:                       n-dodecane (RI 1200), n-pentadecane (RI 1500), n-nonadecane (RI 1900), n-docosane (RI 2200), n-octacosane (RI 2800), n-dotriacontane (RI 3200), n-hexatriacontane (RI 3600)

GC:                                 GC 6890 (Agilent Technologies, Palo Alto, CA, USA)

Injection:                          1 µl splitless, 230°C, 2 min pulse at 110 psi

Column:                           Rtx-5Sil MS, 30 m x 0.25 mm ID with 10 m integrated guard column, 0.25 µm film thickness (Restek GmbH, Bad Homburg, Germany).

Temperature program:       2 min at 80 °C, 15 min ramp to 350 °C, 2 min at 350 °C

Carrier gas:                      Helium, 1 ml min-1, operated by electronic pressure control

MS:                                 Pegasus II TOF-MS system (Leco, St. Joseph, MI, USA), transfer line 250°C, ion source 200°C

Ionization:                        electron impact

Scanning:                         6 spectra s-1 (m/z = 70-600)

Deconvolution:                  AMDIS (Automated Mass Spectral Deconvolution and Identification System, National Institute of Standards and Technology, Gaithersburg, MD, USA)

Settings:                          adjacent peak subtraction (2), resolution (medium), sensitivity (high), shape requirements (high)

 

Remarks:                         Pure reference substances are processed without extraction and fractionation.

Method variants:               - Omission of fractionation for the analysis of a mixed  polar and lipophilic fraction

                                       - Omission of methoxyamination

M[2] (EIQTMS):

Sampling:                         shock freezing in liquid nitrogen

Extraction:                       hot (70°C) methanol/ water/ chloroform (approx. 4:1:2; v/v/v)

Fractionation:                   polar metabolites

liquid partitioning into methanol/water (approx. 1:1; v/v), and chloroform (chloroform phase is discarded).

Derivatization:                   =N-O-CH3  (methoxyamine hydrochloride/ pyridine reagent, 20 mg / ml), -Si(CH3)3  (N-methyl-N-(trimethylsilyl)-trifluoroacetamide, MSTFA)

RI system:                       n-dodecane (RI 1200), n-pentadecane (RI 1500), n-nonadecane (RI 1900), n-docosane (RI 2200), n-octacosane (RI 2800), n-dotriacontane (RI 3200), n-hexatriacontane (RI 3600)

GC:                                 GC 8000 or GC 8000 Top (ThermoQuest, Manchester, UK)

Injection:                          1 µl splitless, 230°C, 2 min

Column:                           Rtx-5Sil MS, 30 m x 0.25 mm ID with 10 m integrated guard column, 0.25 µm film thickness (Restek GmbH, Bad Homburg, Germany).

Temperature program:       1 min at 70 °C, 6 min ramp to 76 °C, 45 min ramp to 350°C, 1 min at 350 °C, 10 min at 330°C

Carrier gas:                      Helium 1 ml min-1

MS:                                 MD 800 MS, Voyager MS or Trace MS (ThermoQuest, Manchester, UK), transfer line 250°C, ion source 200°C

Ionization:                        electron impact

Scanning:                         2 spectra s-1 (m/z = 40-600)

Deconvolution:                  AMDIS (Automated Mass Spectral Deconvolution and Identification System, National Institute of Standards and Technology, Gaithersburg, MD, USA)

Settings:                          adjacent peak subtraction (2), resolution (low), sensitivity (very low –medium), shape requirements (low)

 

Remarks:                         Pure reference substances are processed without extraction and fractionation.

Method variants:               - Omission of fractionation for the analysis of a mixed  polar and lipophilic fraction

                                       - Omission of methoxyamination

 

Citations:

C[1]               Wagner C, Sefkow M, Kopka J (2003).

Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles.

Phytochemistry 62(6) 887-900

C[2]               Colebatch G, Desbrosses G, Ott T, Krussel L, Kloska S, Kopka J, Udvardi M (2004).

Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus.

(in preparation)

 

Sample Contributions:

S[1]               Sefkow M,

Institute of Organic Chemistry and Structure Analysis, Karl-Liebknecht-Str. 24-25, D-14476 Golm, Germany

S[2]               Wagner C, Kopka J,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

S[3]               Draeger B,

Institute of Pharmaceutical Biology, Hoher Weg 8, D-06120 Halle, Germany

S[4]               Richter A,

Institute of Ecology and Conservation Biology, Althanstrasse 14, A-1090 Vienna, Austria

S[5]               Gormann R,

Institute of Pharmacy, Free University of Berlin, Koenigin-Luise Str. 2-4, D-14195 Berlin, Germany

S[6]               Allison G,

Institute of Grassland and Enviromental Research, Sy23 3EB, Aberystwyth, Wales, UK

S[7]               Hause B,

Institute of Plant Biochemistry, Department Secondary Metabolism, Weinberg 3, D-06120 Halle, Germany

S[8]               Desbrosses G*, Udvardi M,

Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Golm, Germany

* Université Montpellier 2, CC 002, Place Eugène Bataillon, F-34095 Montpellier Cedex 05, France

S[9]               Kehr J,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1,  D-14476 Golm, Germany

S[10]             Kraemer U,

Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Golm, Germany

S[11]             Peña-Cortés H,

Centro de Biotecnologia, Universidad Tecnica Federico Santa Maria, Av. Espana 1680, Casilla 110-V, Valparaiso, Chile

S[12]             Kaplan F, Guy CL,

University of Florida, Department of Environmental Horticulture, Gainesville, FL 32611, USA

S[13]             Krueger S, Kopka J,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

S[14]             Kempa S, Hoefgen R,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

S[15]             Schauer N, Roessner-Tunali U*, Fernie A,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

* University of Melbourne, School of Botany, 3010 Victoria, Australia

S[16]             Strelkov S, Schomburg D,

University of Köln, CUBIC - Institute of Biochemistry, Zuelpicher Str. 47, D-50674 Koeln, Germany

S[17]             Wasternak C

Institute of Plant Biochemistry, Department Natural Product Biotechnology, Weinberg 3, D-06120 Halle, Germany

 

Mass spectral Contributions:

MST[1]          Kopka J,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

MST[2]          Schauer N,

Max Planck Institute of Molecular Plant Physiology, Department Prof. Willmitzer, Am Muehlenberg 1, D-14476 Golm, Germany

T_MSRI_ID.txt (version 01.03.2004):

Collection of 855 (1394 version 02) identified or annotated mass spectral tags (MSTs).  This collection contains 632 (796 version 02) non-redundant MSTs of which 229 (241 version 02) are identified.  Mass spectra were manually generated from GC-TOF-MS chromatograms of standard addition experiments or of biological samples.  Each MST has an index number (MPIMP-ID) and a substance name.  Non-identified MSTs are characterized by mass spectral match and name of best matching substance in square brackets.  

Method:                                M[1]

Citation:                                C[1]

 

Q_MSRI_ID.txt (version 01.03.2004):        

Collection of 1166 identified or annotated mass spectral tags (MSTs).  This collection contains 574 non-redundant MSTs of which 306 are identified.  Mass spectra were manually generated from quadrupole GC-MS chromatograms of standard addition experiments or of biological samples.  Each MST has an index number (MPIMP-ID) and a substance name.  Non-identified MSTs are characterized by mass spectral match and name of best matching substance in square brackets. 

Method:                                M[2]

Citation:                               

 

 

 

T_MSRI_NS.txt (version 01.03.2004):

Non-supervised collection of 7534 MSTs obtained by automated deconvolution. 

This collection includes all erroneous deconvolutions and contaminations typically observed in non-sample controls. No signal to noise threshold was applied.

 

Method:                                M[1]

Sample Contribution:       S[2]

MST Contribution:             MST[1]

Citation:                                C[1]

 

Sample Description:

Experiment

Species

Cultivar/Ecotype

Organ

Sample

Fresh

Weight

(mg)

MST number

 

 

 

 

 

 

1135ec03

Non-sample control

 

 

 

265

1135ec23

Non-sample control

 

 

 

201

1135ec61

Non-sample control

 

 

 

132

1135ec05

Arabidopsis thaliana (L.) Heynh.

C24

Leaf

1

368

1135ec24

Arabidopsis thaliana (L.) Heynh.

C24

Leaf

16

450

1135ec06

Arabidopsis thaliana (L.) Heynh.

C24

Root

2

336

1135ec25

Arabidopsis thaliana (L.) Heynh.

C24

Root

10

409

1135ec07

Nicotiana tabacum L.

SNN

Leaf

3

370

1135ec26

Nicotiana tabacum L.

SNN

Leaf

11

445

1135ec08

Nicotiana tabacum L.

SNN

Root

3

306

1135ec27

Nicotiana tabacum L.

SNN

Root

10

477

1135ec13

Solanum tuberosum L.

Désirée

Flower

3

333

1135ec32

Solanum tuberosum L.

Désirée

Flower

10

482

1135ec09

Solanum tuberosum L.

Désirée

Leaf

1

381

1135ec28

Solanum tuberosum L.

Désirée

Leaf

14

424

1135ec10

Solanum tuberosum L.

Désirée

Root

3

369

1135ec29

Solanum tuberosum L.

Désirée

Root

14

399

1135ec12

Solanum tuberosum L.

Désirée

Stolon

3

259

1135ec31

Solanum tuberosum L.

Désirée

Stolon

14

447

1135ec11

Solanum tuberosum L.

Désirée

Tuber

1

272

1135ec30

Solanum tuberosum L.

Désirée

Tuber

18

409

Experimental:

Plants were cultivated on soil in growth chambers with a maximum of 120 µmol photons m-2 s-1 at leaf surface.  Potato (Solanum tuberosum) and tobacco (Nicotiana tabacum) plants were grown in 3 l-pots with a 16 h-light/ 8 h-dark regime changing from 22 °C during the day to 18 °C at night and with relative humidity preset to constant 70%.  Arabidopsis thaliana plants were kept in 0.125 l-pots with identical illumination but changing from 60% humidity and 20 °C during the day to 75% humidity and 18 °C at night.  Samples of plant organs were harvested at 2-6 h in the light period from flowering plants.  Root samples were prepared free of soil but not rinsed with water. 


 Q_LJA_NS.txt (version 01.03.2004):

Non-supervised collection of 6857 MSTs obtained by automated deconvolution. 

This collection includes all erroneous deconvolutions, and contaminations typically observed in non-sample controls. No signal to noise threshold was applied.

 

Method:                                M[2]

Sample Contribution:       S[8]

MST Contribution:             MST[1]

Citation:                                C[2]

 

Sample Description:

Experiment

Species

Cultivar/Ecotype

Organ

Sample

Fresh

Weight

(mg)

MST number

 

 

 

 

 

 

 

 

2236bg10

Lotus japonicus

GIFU B-129

Root lateral

25-50

389

 

2236bg14

Lotus japonicus

GIFU B-129

Root lateral

25-50

318

 

2236bg20

Lotus japonicus

GIFU B-129

Root primary

25-50

481

 

2236bg24

Lotus japonicus

GIFU B-129

Root primary

25-50

511

 

2233bn14

Lotus japonicus

GIFU B-129

Nodule

25-50

42*

 

2233bg08

Lotus japonicus

GIFU B-129

Nodule

25-50

623

 

2233bg14

Lotus japonicus

GIFU B-129

Nodule

25-50

707

 

2336bg54

Lotus japonicus

GIFU B-129

Flower

25-50

449

 

2236bg50

Lotus japonicus

GIFU B-129

Flower

25-50

749

 

2236bg30

Lotus japonicus

GIFU B-129

Leaf developing

25-50

703

 

2236bg34

Lotus japonicus

GIFU B-129

Leaf developing

25-50

593

 

2236bg40

Lotus japonicus

GIFU B-129

Leaf mature

25-50

770

 

2236bg44

Lotus japonicus

GIFU B-129

Leaf mature

25-50

564

 

* partial

 

 

 

 

 

 

 

 

 

 

 

 

 

Experimental:

Lotus japonicus GIFU B-129 seeds were scarified in liquid nitrogen (3x10 sec), sterilized in a 2% bleach solution for 10 minutes, rinsed five times with sterile distilled water, then germinated and grown in coarse quartz sand in a controlled environment (16 h day, 60% relative humidity, and 21/17°C day/night temperate regime). Pots were watered daily with 1/4 B&D medium.  Plants were inoculated when 7 days old with Mesorhizobium loti strain R7A and provided with 1mM KNO3 for the first 2-3 weeks of growth.  Plant organs were harvested at 12-weeks, collected directly into liquid nitrogen, and stored at -80°C.  At each harvest plants were carefully pulled from the quartz sand and a complete set of 6 organ samples prepared, i.e. nodules, lateral and primary root, mature and developing leaves, and flowers.  Leaves were separated according to morphological criteria into a group of young expanding leaves from the apex of the plant and a group of mature fully expanded leaves from the middle of the plant shoot.  Senescent leaves were discarded.  Whole flowers were prepared including all floral organs, petals, sepals, carpels, stamen, and pollen.  Lateral roots without visible nodule primordia were collected, followed by pink nodules sampled in a representative range various sizes. The harvest was completed by preparing the primary root, i.e. 2 cm of the main root directly below the hypocotyl.  Only samples without nodules and lateral roots were collected. 


Q_LYC_NS.txt (version 01.03.2004):

Non-supervised collection of 15386 MSTs obtained by automated deconvolution. 

This collection includes all erroneous deconvolutions, and contaminations typically observed in non-sample controls. No signal to noise threshold was applied.

 

Method:                                M[2]

Sample Contribution:       S[15]

MST Contribution:             MST[1], MST[2]

Citation:                               

 

Sample Description:

Experiment

Species

Cultivar/Ecotype

Organ

Sample

Fresh

Weight

(mg)

MST number

 

 

 

 

 

 

 

 

04019a49

Lycopersicon esculentum

M82

Root

100

474

 

04019a50

Lycopersicon esculentum

M82

Root

100

525

 

2352AI05

Lycopersicon esculentum

M82

Leaf

100

484

 

2352AI10

Lycopersicon esculentum

M82

Leaf

100

710

 

3090AU02

Lycopersicon esculentum

M82

Green fruit

200-250

467

 

3090AU10

Lycopersicon esculentum

M82

Green fruit

200-250

470

 

3090AU05

Lycopersicon esculentum

M82

Orange fruit

200-250

458

 

3090AU13

Lycopersicon esculentum

M82

Orange fruit

200-250

433

 

3090AU09

Lycopersicon esculentum

M82

Red fruit

200-250

508

 

3090AU17

Lycopersicon esculentum

M82

Red fruit

200-250

422

 

03363a02

Lycopersicon pennellii

 

Fruit 45DAF*

200-250

349

 

03363a03

Lycopersicon pennellii

 

Fruit 45DAF

200-250

451

 

03363a10

Lycopersicon chmielewskii

 

Fruit 45DAF

200-250

475

 

03363a11

Lycopersicon chmielewskii

 

Fruit 45DAF

200-250

431

 

03363a08

Lycopersicon hirsutum

 

Fruit 45DAF

200-250

410

 

03363a09

Lycopersicon hirsutum

 

Fruit 45DAF

200-250

392

 

03363a06

Lycopersicon parviflorum

 

Fruit 45DAF

200-250

397

 

03363a07

Lycopersicon parviflorum

 

Fruit 45DAF

200-250

379

 

03363a04

Lycopersicon pimpinellifollium

 

Fruit 45DAF

200-250

384

 

03363a05

Lycopersicon pimpinellifollium

 

Fruit 45DAF

200-250

382

 

3268au03

Lycopersicon pennellii

 

Leaf

100

461

 

3268au15

Lycopersicon pennellii

 

Leaf

100

578

 

3268au31

Lycopersicon chmielewskii

 

Leaf

100

615

 

3268au37

Lycopersicon chmielewskii

 

Leaf

100

688

 

3268au06

Lycopersicon hirsutum

 

Leaf

100

657

 

3268au18

Lycopersicon hirsutum

 

Leaf

100

731

3268au16

Lycopersicon parviflorum

 

Leaf

100

689

3268au28

Lycopersicon parviflorum

 

Leaf

100

710

3268au05

Lycopersicon pimpinellifollium

 

Leaf

100

602

3268au29

Lycopersicon pimpinellifollium

 

Leaf

100

689

 

 

 

 

 

 

 

*DAF (days after flowering)

 

Experimental:

Tomato plants of accession numbers LA1589 (L. pimpinellifolium), LA2133 (L. parviflorum), LA1028 (L. chmielewskii), LA1777 (L. hirsutum) and LA0716 (L. pennellii) were obtained from the true-breeding monogenic stocks maintained by the Tomato Genetics Stock Centre (University of California, Davis). The plants were grown on soil in a growth chamber with 500µmol photons m-2s-1 at 25°C/day and 20°C/night under a 12h day/ 12h dark regime. Experiments were carried out on mature fully expanded source leaves from six week-old-plants and on fruits taken 45 days after flowering. Tomato plants of accession number LA3475 (Lycopersicon esculentum), also obtained from the Tomato Genetics Stock Centre (University of California, Davis), for collection of fruits and leaf material were grown in green house under a minimum of 250µmol photons m-2s-1 at  22°C and 20°C/night.

Samples were taken 6 h into the light period from mature fully developed leaves of 6-week-old plants. Fruit samples were taken 21DAF, 42DAF and at breaker stage exclusively from pericarp tissue after rapid removal of the epidermis.

Root samples were taken 6h into the light period from hydroponically grown tomato plants of accession number LA2706  (Lycopersicon esculentum cv. Moneymaker). Plants were grown in tomato complete solution (Ca(NO3)2 1,25Mol m-3, KNO3 1,5 Mol m-3, MgSO4 0,75Mol m-3, K2HPO4 0,83Mol m-3, FeEDTA 0,05Mol m-3, H3BO3                              11,6µmol m-3, MnSO4         2,4µmol m-3, ZnSO4                             0,2µmol m-3, CuSO4                  0,1µmol m-3, NaMoO4    0,1µmol m-3) under a 16h day/ 8h night regime with 250µmol photons m-2s-1 at 22°C/day and 20°C/night.