Title: PG3.51 Mass Spectrometry School of Chemistry
1PG3.51Mass Spectrometry School of Chemistry
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3Overview
- Data acquisition
- HT
- Manual
- Ionisation
- LR
- HR
- High MWt
- Data analysis
- Web-based sample submission and data review
4High Throughput
Analysis time short reaction monitoring, fragile
samples Immediate access during working
day Multiple ionisation options to fit diverse
chemistries Generic methods not optimised to
your specific sample Sample overload should not
be an issue if correct amount submitted by user
5Manual
Method specific conditions optimised to specific
samples Correct ionisation method guaranteed Data
integrity assured interpretation not constrained
by pre-conceptions Slow dependent on staff and
instrument time
6Ionisation
Gas phase Electron Ionisation (EI) Generic
gas phase ionisation Information rich
spectra No molecular ion Chemical Ionisation
(CI) Gas phase basicity driven
ionisation Protonated molecule observed False
representation of sample Data more difficult to
interpret Condition dependent data
7Ionisation
Solution phase Electrospray Ionisation (ESI)
Simple data positive ion - protonated or
cationised molecule negative ion - deprotonated
molecule Requires basic or acidic site in the
molecule for ionisation Ionisation not
quantitative Atmospheric Pressure Chemical
Ionisation (APCI) Less restrictions on
functionality of molecule Not applicable to
large molecules Generic method
8Low Resolution MS
HT methods Compromised sample ionisation or
introduction GC interface competitive
ionisation for API
9High Resolution MS
Can resolve nominally isobaric species Accurate
mass - gives elemental composition of the ion
measured Is not equivalent to elemental
analysis Slow Different ESI source different
ionisation Not appropriate for impure
samples High mass cut-off of m/z 1000
10High Molecular Weight Molecules
Dedicated HT instruments Platform and
MALDI-TOF Needs in-depth training Good data
related to user knowledge Data analysis training
and processing time-consuming HT options are
generic methods Additives used compromise small
molecule analysis on Platform
11Data Analysis
Web based system consistent and correct data
processing View the data and interpret all ions
are there for a reason Time wasted reprocessing
can lead to misrepresentation of results
Impurities contaminants often ignored (these
can compromise ionisation) see www.soton.ac.uk/ms
web for info
12Web-based Sample Submission and Data Review
- Unique and secure single user accounts
- Networked computer within soton.ac.uk domain
- Save address in internet browser for access to
RemoteAnalyzer - http//152.78.196.1189999/RemoteAnalyzer/login.a
spx - Launch internet browser
13A current view of the mass spectrometer
Black Box
14ESI
MALDI
LC/MS
LC/MSMS
ESI
CZE/MS
ESI
Ion trap
TOF
QTOF
Quad.
FT-ICR
ESI
Waters
Bruker
AB-Sciex
Kratos
Thermo
Problem too many black boxes
15 - In his book, Rays of Positive Electricity
(1913), J.J.Thomson remarked - I feel sure that there are many problems in
chemistry which could be solved with far greater
ease by this than by any other method. The
method is surprisingly sensitive, ..requires an
infinitesimal amount of material and does not
require this to be specially purified.
16 17 - How sensitive?
- Spectrum from 1 ng
- Actually possible from 10 pg
- Can use less
- 500 amol
18 - Introduction
- What is a mass spectrometer?
- This is an instrument that operates under vacuum
and separates charged gas phase species according
to their mass-to-charge ratio. - How does this help you?
- There are a variety of different types of mass
spectrometer available. These employ various
ionisation techniques and mass analysers that
allow a wide range of molecules to be analysed
from gases and small organic molecules through
the mass range to large biopolymers.
19Chemistries studied
-
- Combichem
- Inorganic
- Natural product synthesis
- Bio-Organic
- Small Organic
- Peptides
- Proteins
- Polymers
- Biopolymers
- Organometallics
20Mass Spectrometry
- Instrumentation available
- VG Analytical 70-250-SE Normal geometry
double focusing MS. - Micromass TofSpec2E Reflectron
MALDI-TOFMS. - ThermoQuest TraceMS Single quadrupole
GC-MS. - Bruker ApexIII FT-ICR-MS.
- ThermoBioAnalysis Dynamo Linear MALDI-TOFMS.
- Micromass Platform II Open access single
quadrupole MS. - Waters ZMD Open access single quadrupole
MS. - ThermoQuest TraceMS Open access single
quadrupole GC-MS. - ThermoFinnigan LCQ Ion trap.
- Micromass PlatformLC Single quadrupole MS
21How do I determine the method of analysis?
- Consider which of the following is appropriate
- ionisation technique(s)
- sample introduction method
- analyser type and why
- why not other systems
- sample preparation
- what ions would you expect to see in the mass
spectrum
22Introduction
- What is a mass spectrometer?
23What do I do?
- Which system do you use?
- Which ionisation process is appropriate?
- This is dependant on the nature of the sample
- ve or -ve ionisation?
- Again this is dependant on sample type
24Sample Introduction
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30Multiuser Waters ZMD ES, APCI, FIA or
HPLC ThermoQuest TraceMS EI, CI, NICI
GC-MS Micromass Platform II ES,
APCI ThermoBioAnalysis Dynamo MALDI
online HPLC optional off-line infusion ES
MS optional off-line You must be trained by
either GJL or JMH
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32MS only VG Analytical 70-250-SE LREI, LRCI,
LRFAB, HREI, HRCI, HRFAB HR-GC-MS. Micromass
TofSpec2E MALDI, maybe HRMALDI in future. Bruker
ApexIII ES, MSn, HPLC-MS, NS.
33How to submit samples for open access systems
- API
- 1 mg mL-1 in 1 mL of appropriate solvent,
preferably MeCN or MeOH - 2CV vial with teflon disk snap-cap top
- Microtitre plates (ZMD)
- EI/CI-GC-MS
- 10 mg mL-1 in 1 mL of appropriate solvent,
preferably DCM - 2CV vial with butyl septa crimptop
34How to submit samples for MS service
- Complete, in full, form and complete XL sheet in
login area - MS form available from website www.soton.ac.uk/ms
web - incomplete forms will be returned without analysis
35How to submit samples for MS service
- Fill in the sample progression sheet (XL)
- LR-MS (If open access is not appropriate)
- 1 mg of material in a screw-top vial clearly
labelled, if in solution then state solvent and
concentration hazard info - HR-MS
- EI/CI 1mg of pure sample (accurately weighed),
clearly labelled with weight recorded on vial. - ES 10 µg mL-1 solution in MeOH or MeCN.
- LR-MS reference number info.
36- Simple Dos Donts
- Do not use any system unless you have been
trained by GJL/JMH - Label your bottle clearly, with a systematic
reference number - Remove your samples from the autosampler/Lab
promptly after analysis - Please spend time and clearly complete forms in
full - Do not hoard samples and submit in batches,
especially HR at end of your final year - If possible do not keep submitted samples in your
labs - Use the MS clinics, they are there to help you
37MS Clinics
- What are they?
- Daily help sessions between 11.30-12.00 and
15.00-15.30 - How do you use them?
- Where appropriate, check data by reprocessing.
- Bring Spectra, MS file reference, structure,
calculated mass and any other supporting
information - Come with a specific question
38 If in doubt ask us or E-mail msweb_at_soton.ac.uk
Julie Herniman John Langley 30 years
experience in MS Classically trained mass
spectrometrists Experience of MS vast array of
chemistries Departmental Commercial School
knowledge base for MS
39 40Atomic Structure
e-
e-
e-
Protons Neutrons
e-
e-
e-
Particle Mass, amu Charge Electron 0.00055
-1 Proton 1.0073 1 Neutron 1.0087 0
41 42Isotopes
mass number protons neutrons
C
C
12
13
6
6
atomic number protons
Atoms with the same atomic number but different
mass numbers are called isotopes.
43Atomic Weights
Natural Abundance
Mass, amu
Symbol
Carbon 12C 12.0000
98.89 13C
13.0033 1.11 Chlorine
35Cl 34.9689 75.77
37Cl 36.9659
24.23 Mass assigned as exactly 12
by international agreement
Atomic weight (C) 0.9889(12.0000)
0.0111(13.0033) 12.011 Atomic weight (Cl)
0.7577(34.9689) 0.2423(36.9659) 35.453
44Molecular Weights
Calculation of the MW of Reserpine, C33H40N2O9
Using Atomic Weights Using Single
Isotopes C 33 x 12.011 396.363 C
33 x 12.0000 396.000 H 40 x 1.0079
40.316 H 40 x 1.0078 40.312 N
2 x 14.0067 28.013 N 2 x 14.0031
28.006 O 9 x 15.9994 143.995 O
9 x 15.9949 143.954
608.687
608.272
45Isotope Ratios
C1 C10 C100
m/z R.I. X 100 X1 110 X2
60 X3 22
m/z R.I. X 100 X1 1.1
m/z R.I. X 100 X1 11.0
R.I.
m/z
46Isotope Ratios, cont.
Cl1 Cl2 Cl3
m/z R.I. X 100 X2 97.5 X4
31.7 X6 3.4
m/z R.I. X 100 X2 32.5
m/z R.I. X 100 X2 65 X4 10.6
R.I.
m/z
47Isotope Ratios, cont.
Br1 Br2 Br3
m/z R.I. X 34 X2 100 X4
98 X6 32
m/z R.I. X 100 X2 98
m/z R.I. X 51 X2 100 X4 49
R.I.
m/z
48 - Questions
- What is meant by resolution?
- The ability of a mass spectrometer to
distinguish between ions of different mass to
charge ratio values is termed as resolution. A
mass spectrometer has the ability to measure
isotopic masses, e.g. the mass spectrum of HCl
will show two peaks, nominally at 36 Da and 38 Da
at an approximate ratio of 31, not at the
average chemical mass of 36.5.
49 36.5
50 51 What is meant by isotopic mass, average mass
and nominal mass?
-
- Consider a given empirical formula, e.g.
C60H122N20O16S2. - The average mass, calculated using the average
atomic mass 1443.8857 Da. - The monoisotopic mass, calculated using the
exact mass of the most abundant isotopes
1442.8788 Da. - The nominal mass, calculated using the integer
mass of the most abundant isotopes 1442 Da. - Which mass do you use?
- This depends on the resolving power of the MS
and the mass of your molecule in general for
small molecules use isotopic masses.
52 - Introduction
- What is a mass spectrometer?
53 - Analysers
- Sector Instruments
- Quadrupole Analysers
- Time-of-Fight (TOF)
- Ion Traps
54 - Analysers
- Sector Instruments
- Original instruments based on fixed field
magnets. Introduction of second sector, the
electrostatic analyser and the electromagnet
increased the resolution and mass range of the
instruments. Magnet sector machines operate as
low resolution and high resolution instruments
and can be constructed as either normal geometry
or reverse geometry machines. The configuration
affects the ultimate resolution and also the MSMS
capabilities of the instrument. Sector machine
operate with high voltages on the ion sources,
commonly 8kV.
55 - Analysers
- Quadrupole Analysers
- Four concentric rods wired in pairs with
alternating rf dc voltages applied. Ions that
undergo stable oscillations are separated
according to their m/z ratio and detected. The
majority of quad systems are low resolution
instruments they do not operate at high voltages
and because analysis is achieved by switching of
voltages is capable of fast scanning and
consequently are ideally suited to interfacing to
GC, HPLC, CEC and CE.
56 - Analysers
- Time-of-Fight (TOF)
- Probably the simplest type of mass analyser. As
the name suggests it measure the time it takes
an ion to travel a specific distance. The ion is
initially accelerated by a high potential
20-30kV, different mass ions will be accelerated
into the analyser with initial velocities
proportional to their masses and subsequently
arrive at the detector at different times. The
advent of DE (PE, TLF) has improved the
resolution of these systems. Similarly
reflectron systems produce higher resolution data
than linear systems. ES-TOFs, GC-TOFs and
hybrid instruments have recently become available.
57 - Analysers
- Ion Traps
- The ion trap functions both as an analyser and
an ion storage device. The ions are produced or
introduced into the ion trap, trapped and can be
progressively ejected form the ion trap volume
by ramping of the rf voltage. The trapped ion
can also be induced to undergo dissociation and
hence produce the MSMS spectrum within the one
analyser. Note the difference with FT-ICR-MS
where the frequency of the circulating ions is
measured and Fourier Transformed in give the MS.
58Mass 28 on a quad - unit resolution
100
28.00619
90
80
70
60
Intensity (age)
50
40
30
20
10
0
59Low resolution on a sector - R 1000
60High resolution on a sector - R 10 000
61Comparison in ion profiles
62MS HV scan _at_ R 10000 (uncalibrated)
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65 - Introduction
- What is a mass spectrometer?
66Ionisation Techniques
- Electrospray (ESI)
- Electron Ionisation (EI)
- Chemical Ionisation (CI)
- Matrix-Assisted Laser Desorption/Ionisation
(MALDI) - Atmospheric Pressure Chemical Ionisation (APCI)
- Fast Atom Bombardment (FAB)
- Others
67Electrospray ionisation source
68- Electrospray Ionisation (ESI)
- This is a very mild, solution based ionisation
process. It relies on the analyte having either
a basic site or acidic site for ionisation. The
eluent is sprayed at a high electropotential. - M (sol) ? (M nH)n
- In the case of singly charged ions signals are
observe for the protonated molecule or cationised
molecule - (M X) where X H, NH4, Na, K.
- For larger molecules then multiple charging can
take place. Note that within the multiple charge
envelope the charge states will be incremental,
i.e. vary by 1. The true mass of the molecule
can be obtained by solving the simultaneous
equations or by using one of the many
deconvolution packages available with the
instruments.
69Electrospray ionisation process
M (sol) ? (M nX)n (gas phase) M (sol) ?
(M - nX)n- (gas phase) where X H, NH4, Na, K.
70Electron ionisation process
71- Electron Ionisation (EI)
- Ionisation by electron bombardment on a
gas-phase molecule is an inelastic process the
ionising electron loses some of its kinetic
energy to the molecule, part of which is carried
of by the secondary electron released on
ionisation, and part of which is retained by the
newly formed ion as internal energy. In a
population of molecules a distribution of
energies is transferred, as illustrated in the
figure. The ionisation energy (IE) is the minimum
energy required to ionise a molecule, typically
about 8 - 12 eV for most organic compounds, so
molecules acquiring energies greater than IE will
be ionised. The appearance energy is the minimum
energy needed for ionisation and reaction to form
a fragment ion, and for a simple bondbreaking
reaction this may be 2 or 3 eV above the
ionisation energy. Each possible reaction path
will have its own characteristic AE.
72- Electron Ionisation (EI)
- Gas phase molecules are bombarded with a stream
of electrons to produce a radical cation. This
is a harsh ionisation technique. - M (g) e ? M. (g) 2e
- The molecular ion (MI) can undergo fragmentation
- M. ? F R.
- M. ? F. nm
- The Fragment ions can also undergo
fragmentation - F. ? F1 R.
- F ? F1 nm
73- Stability of the Molecular Ion
-
- If the mass spectrum shows a strong molecular
ion peak this means the ion can stabilise the
charge effectively. This is often the case for
aromatic compounds, which give large molecular
peaks and few fragment ion peaks. Benzene has its
base peak (100 relative abundance) at m/z 78
there are no major fragment peaks, the molecular
ion representing more than 50 of the total ion
current. - This is because ionization of benzene can be
achieved by removal of an electron from the
delocalized pi-system, without seriously
weakening the structure, and the ion thus formed
can delocalise the charge over the whole
molecule. - By contrast, ionisation of the saturated
cycloalkane cyclohexane can only be through loss
of a sigma-electron, leaving a weak C-C or C-H
single-electron bond. The molecular ion at m/z 84
is not the base peak, and it represents less than
20 of the total ion current
74- Fragmentation and Fragment Ion Stability
- Electron ionisation mass spectrometric reactions
occur at low pressure in the gas phase and are
unimolecular. They can be sequential or they may
occur in parallel. - In a complex spectrum there will be a network of
competing and consecutive reactions, but a simple
spectrum such as that of acetone shows only three
significant peaks and this may conform to one of
these schemes.
75- Fragmentation and Fragment Ion Stability
- Chemical reactions are controlled by both
thermodynamics and kinetics, and whether the
majority of molecular ions break down to fragment
ions will depend not only on their energy but
also on the time available for reaction. This
time is the period spent in the ion source, which
is typically 1us. This is a long time in relation
to bond vibrations and will be adequate for
simple bond breaking reactions. - However, complex rearrangements may require the
ions to attain shapes that are difficult to
achieve, and such reactions may take longer than
1us. This means that some fragment ions formed by
high energy pathways could be more abundant in
the spectrum than other ions formed by low energy
pathways the latter are dependent on a
rearrangement. -
76- Fragmentation and Fragment Ion Stability
- Energetically the McLafferty rearrangement is
more favourable, and yet because of steric
requirements make it slower than the simple bond
breaking reaction. Many of the molecular ions
will undergo the bond breaking reaction before
they have had time to undergo the McLafferty
rearrangement. - It is frequently the case that rearrangement
ions are favoured on energetic grounds as they
are formed in processes that involve bond
formation as well as bond breaking. Energy is
required to break bonds, therefore energy is
given back in the making of new bonds. - The McLafferty rearrangement is just one of many
types of rearrangements.
77- Fragmentation and Fragment Ion Stability
- In considering fragmentation mechanisms it is
generally assumed that the site of the charge is
located at a specific site in the ion, and that
this will initiate the reaction. A complex
molecule with more than one functional group may
be ionised at a number of different sites, giving
different types of ion and different types of
reaction. - The site of ionisation will then be reflected in
the origin of the peaks in the mass spectra.
78Chemical ionisation process
79- Chemical Ionisation (CI)
- The reagent gas reacts exothermically with the
molecule M, behaving as a strong Bronsted acid,
giving the protonated molecule MH -
- The proton affinities of methane and ammonia
are respectively 551 and 854 kJ/mol so that the
transfer of a proton from CH5 to an organic
molecule is always quite exothermic, giving rise
to appreciable fragmentation. - For less basic substances, such as
oxygen-containing compounds, on the other hand,
the transfer of a proton from the NH4 ion to the
sample molecule is endothermic and therefore will
not occur. Instead, the reactants form an adduct
which usuallv undergoes limited fragmentation. - The analyte must have a greater proton affinity
(gas phase) than the reagent gas ions for proton
transfer to take place. In some cases adduct
ions are formed for compound containing a large
number of functional groups. -
80- Chemical Ionisation (CI)
- A reagent gas is used and is bombarded with a
stream of electrons to produce a radical cation.
- RG (g) e ? RG. (g) 2e
- The reagent gas MI, e.g. ammonia, undergoes
collision with neutral reagent gas - NH3. NH3 ? NH4 NH2.
- Proton transfer takes place between the
protonated ammonia (in excess) and the analyte M - NH4 M ? MH NH3
- With ammonia the adduct ions can also be formed
- NH4 M ? MNH4
81- Chemical Ionisation (CI)
- CI is a softer ionisation technique than EI,
some fragmentation may occur. - Note
- MNH4 - H2O has the same nominal mass as M
- Rarely do you see radical cations in CI spectra
unless there is a problem with the gas supply or
ion source. - Only use CI if you do not observe the MI by EI.
-
82Chromatogram
Peak Retention Time
Spectrum
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84MALDI
85MALDI
86MALDI
87 - Matrix-Assisted Laser/Desorption Ionisation
(MALDI) -
- The sample is mixed with a UV absorbing matrix,
the latter in great excess. Singly charged
protonated and/or cationised molecules are
produced, hence the need for a large mass range
analyser. Also good for involatile small
molecules, peptides, biopolymers and polymers.
Used in conjunction with TOFs to give large mass
range. - Uses pmols of material.
88MALDI ionisation process?
M (solid) ? (M X) (gas phase) M (solid)
? (M -X)- (gas phase) where X H, NH4, Na, K.
89 - MALDI Contamination Limits
- Analysis is relatively insensitive to
contaminants. - Phosphate 20 mM EDTA 1 mM
- Detergents 0.1 Glycine 20 mM
- Glycerol 2 Sodium Citrate 20 mM
- Buffer (Tris) 50 mM K phosphate 25 mM
- Guanidine 1 M Na phosphate 0.1M
- Na azide 1 Octyl glucoside 0.3
- SDS 0.05 Ammon. Bicarb. 0.1M
- Suggested concentrations
- 10 pmol _at_ lt10 000 Da (pure)
- 100 pmol _at_ gt50 000 Da (pure)
90 - Atmospheric Pressure Chemical Ionisation (APCI)
-
- Very similar to ES, except that the spray is
neutral and passes through a corona discharge.
Singly charged protonated molecules are produced.
Ionisation is not so dependent on the
functionality of the analyte cf. ESI, though some
functionality is required. -
91 - Ionisation Techniques
- EI CI are gas phase processes, therefore the
sample must be volatile and thermally stable. - ES, APCI MALDI are condensed phase techniques,
therefore the samples must be soluble. - E.g. MeCN, MeOH, H2O or mixtures of these.
- Do not use involatile buffers for spray
techniques.
92- Now we can answer some questions
- Which ionisation process is appropriate?
- This is dependant on the nature of the sample.
- Functionality, volatility (MP/BP), size.
- ve or -ve ionisation?
- Again this is dependant on sample type.
- Functionality, pH of solution.
93- Determine the method of analysis
- Consider which of the following is appropriate
- ionisation technique(s)
- sample introduction method
- analyser type and why
- why not other systems
- sample preparation
- what ions would you expect to see in the mass
spectrum
94 - Ionisation Techniques
- EI CI are gas phase processes, therefore the
sample must be volatile and thermally stable. - For OA EI, CI GCMS rmm lt 500Da, MP lt 150 oC
- Solvents DCM, EA, cHexane. NOT aqueous.
- ES, APCI MALDI are condensed phase techniques,
therefore the samples must be soluble. - For OA ES APCI use MeCN, MeOH, H2O or mixtures
of these. - Do not use DMF, DMSO or THF, check with GJL or
JMH if other solvents are used. - Do not use involatile buffers.
95 - Interpretation
- How do I interpret my spectra?
- Check the quality of the data does the total ion
chromatogram look ok? - Does the mass spectrum show significant peaks
above the baseline? - Identify any major peaks.
- Look for telltale isotope patterns.
- Remember the Nitrogen Rule. (The Nitrogen Rule
A neutral compound containing an odd number of
nitrogen atoms will always have an odd molecular
mass.) - Do the masses fit with the proposed structure?
- Have you used the appropriate masses in your
calculations?
96 - Interpretation
- How do I interpret my spectra?
- Identify the MI
- Check isotope pattern - halogens, sulphur, tin
etc. - Odd/Even Mass - Nitrogen Rule
- If EI check intensity of MI - aromatic or
aliphatic - Accurate mass - calculate r db
- CxHyNzOn
- r db x - 0.5y 0.5z 1
- whole number OE
- even number EE
97- Reporting Data
- State method, ionisation mode, e.g.
- LRMS (EI) m/z 220, 80 (M.) 205, 100
(M-CH3) - HRMS (ES) Found 501.1234 Da (M H),
calculated 501.1238 Da - You should report the Base Peak (BP), Molecular
Ion (MI) or protonated or cationised molecular
ion(s) (M X) and any other significant peaks.
For EI spectra the eight major peaks are
considered representative. - Remember higher mass ions of low intensity can be
more important that high intensity low mass ions.
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111 C H N O mass
DBE error . Mass Analysis for mass
304.1540660 1 17 22 1 4
304.1543346 7.5 8.832e-07 2 2 18
13 5 304.1548372 0.5 2.535e-06 3
15 20 4 3 304.1529919 8.0
3.531e-06 4 18 18 5 0
304.1556720 12.5 5.280e-06 5 4 20
10 6 304.1561798 0.0 6.950e-06 6
14 24 0 7 304.1516545 3.0
7.928e-06 7 13 18 7 2
304.1516493 8.5 7.946e-06 8 20 20
2 1 304.1570147 12.0 9.695e-06 9
5 16 14 2 304.1575172 5.0
1.135e-05 10 6 22 7 7
304.1575225 -0.5 1.136e-05 Â Mass
Analysis for mass 182.1176340 1 10 16
1 2 182.1175552 3.5 4.328e-07 2
8 14 4 1 182.1162125 4.0
7.805e-06 3 7 18 0 5
182.1148751 -1.0 1.515e-05 4 6 12
7 0 182.1148698 4.5 1.518e-05 5
5 16 3 4 182.1135324 -0.5
2.252e-05 6 0 12 11 1
182.1220805 0.5 2.442e-05 7 3 14
6 3 182.1121898 0.0 2.989e-05 8
2 14 8 2 182.1234232 0.0
3.179e-05 9 1 12 9 2
182.1108471 0.5 3.727e-05 10 4 16
5 3 182.1247658 -0.5 3.916e-05