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MB Sample ID: SA011784

Local Sample ID:A_M1e
Subject ID:SU000278
Subject Type:Bacterial cells
Subject Species:Sinorhizobium meliloti
Taxonomy ID:382
Genotype Strain:Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917
Human Ethnicity:wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a tRNAarg and the smb20996-engA operon from pSymB were integrated to chromosome in strains RmP3009 and RmP2917
Species Group:Microorganism

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Subject:

Subject ID:SU000278
Subject Type:Bacterial cells
Subject Species:Sinorhizobium meliloti
Taxonomy ID:382
Genotype Strain:Rm2011 (SU47 str-3)|SmA818|RmP3009|RmP2917
Human Ethnicity:wild type|Rm2011 lack pSymA|Rm2011 lack pSymB|Rm2011 lack pSymA and pSymB | a tRNAarg and the smb20996-engA operon from pSymB were integrated to chromosome in strains RmP3009 and RmP2917
Species Group:Microorganism

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
A_M1eSA011784FL002928ΔpSymAstrains

Collection:

Collection ID:CO000271
Collection Summary:-
Sample Type:cells
Volumeoramount Collected:6 x 108 cells
Storage Conditions:-80ºC freezer
Collection Vials:eppendorf tube
Tissue Cell Identification:6 x 108 cells

Treatment:

Treatment ID:TR000291
Animal Vet Treatments:-80ºC freezer
Animal Anesthesia:test tube
Animal Endp Tissue Proc Method:M9 miminal medium plus 10 mM sucrose
Animal Endp Clinical Signs:n/a
Human Fasting:30ºC incubator
Human Endp Clinical Signs:OD600 values of approximately 0.3, 0.5, 0.9, 1.6, and 3.5 (except for Rm2011 which reached ~4.8)

Sample Preparation:

Sampleprep ID:SP000285
Sampleprep Summary:-
Sampleprep Protocol Filename:Fei,_F.,_Bowdish,_D._M._E.,_&_McCarry,_B._E._(2014)._Analytical_and_Bioanalytical_Chemistry,_406,_3723–3733.
Extraction Method:cell pellet extracted with 2:2:1 MeOH/EtOH/H2O with beadbeating
Extract Storage:-80ºC freezer
Sample Resuspension:cell extracts suspended 60%v/v acetonitrile/water
Sample Spiking:L-methionine-d3, L-tryptophan-d5 as standards for recovery determination ; L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine as internal standards for peak area normalization
Cell Type:Gram negative bacterium

Combined analysis:

Analysis ID AN000409 AN000410
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1200 RR Series II Agilent 1200 RR Series II
Column Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Bruker MicrOTOF II Bruker MicrOTOF II
Ion Mode POSITIVE NEGATIVE
Units normalized peak area normalized peak area

Chromatography:

Chromatography ID:CH000290
Methods Filename:Opt_silicaHILIC.m
Instrument Name:Agilent 1200 RR Series II
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Column Temperature:40C
Flow Gradient:0-0.5 min, 95%A; 0.5-12.5 min, 35%A; 12.5-13.0 min, 35%A; 13.0-14.0 min, 95%A; 14.0-24.0 min, 95%A
Flow Rate:200 ?L/min
Internal Standard:L-phenylalanine-d8, diphenylalanine and glycine-phenylalanine
Sample Injection:2 ?L
Solvent A:100% acetonitrile
Solvent B:100% water;10 mM ammonium acetate, adjust to pH 3 with formic acid
Analytical Time:24 min
Chromatography Type:HILIC

MS:

MS ID:MS000351
Analysis ID:AN000409
Instrument Name:Bruker MicrOTOF II
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
Capillary Voltage:-3800 V
Dry Gas Flow:8.0 L/min
Dry Gas Temp:250ºC
Scan Range Moverz:50-1000 m/z
  
MS ID:MS000352
Analysis ID:AN000410
Instrument Name:Bruker MicrOTOF II
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Voltage:4500 V
Dry Gas Flow:8.0 L/min
Dry Gas Temp:250ºC
Scan Range Moverz:50-1000 m/z
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