5th AMS User’s Mtg Analysis Tutorial

Loading:

Check analog inputDefault list in shift-m window for easy access (can change to match your

preferences)

Browse for data and load (all or first run + new)Instrument diagnostics graph appears

MS time trends, uncheck ms correction factors and calculate time series using default

• check to see if anything is seriously out of whack• NH4 not too far off, there’s some water, etc.

Ms tab: check ‘auto update’Load tab: ‘do auto update’TOF tab: check ‘auto update’ (see next slide for settings)

Panel SettingsLoad settings TOF update settings

Approximate chopper width

Can’t use this until corrections calculated

Instrument Diagnostics• Duty cycle should be ~80% b/c of dead time when switching btw ms and tof; can be larger if

doing analysis on acquisition computer• Flowrate jump b/c measuring backup pump, not lens – discard in this case (pt 203, run 5905)

[Time types: pt num (igor indexing), run num (ams saving), date/time (display)]• Calibrations clear when mult voltage, gain, and ion eff change (heater bias indicates balzers

tuning)• Increase in AB b/c of pump down (multiplier outgassing, ionizer)• Choose period to do calibrations – want steady state, so pick afternoon 7/11 –next slide

‘Automatic’ graphs that are updated for each loading when set ‘Auto Update’ in MS and TOF tabs

One more daySome small particle events already visible

Corrections

•Select period afternoon 7/11 (runs 6043-6048)

•Right click and SetRunInterval•Values automatically appear in Corrections tab

•Check ‘Auto-set’•After calculated and correction factors appear, uncheck ‘Auto-set’ so don’t accidentally reset the corrections

Air Correction

No ms correction factors

With ms correction factors

‘Air’ is combination of gas-phase contributions from all species, so doesn’t go to straight line.

Effect of AB and flowrate corrections

• AB used to calculate ug/s and flow used to determine ug/m3 (volume).• Velocity cal valid for only one point on flowrate curve, so to be really precise, have

to account for that (especially on airplane)• Pressure/Flow measurement is mass flow • Always uses dynamic flowrate over time to tweak airbeam (not single value shown

in corrections panel), assumes change in flowrate and ab is linear (i.e., if flow changes 2%, then AB changes 2%)

Flowrates 2 (Sunday)• Volumetric flowrate – proportional to sqrt T

• Ambient mass/volume basis• Critical orifice creates volume flowrate (m3/s) that is cnst w/ pressure and

depends only on sqrt T• Measure volume at known pressure and temperature• Suggest measure lens pressure (mass measurement) and sampling line pressure

and temperature• So only changes w/ orifice size (clogging)

• Mass flowrate – proportional to P/sqrt T• Physically measure w/ instrument pressure which is proportional to amt of

mass entering critical orifice every second• Calibrate to get volume flowrate• Value reported by software is volume of air at conditions baratron calibrated at

(T and P). If at sea level, etc. get STP volumetric flowrate• Basis of AB correction – flux of molecules entering detection region doesn’t

change• Get ug/m3 at calibration temperature and pressure (typically STP)

• Bahreini et al., 2003

Flowrate 3 (Sunday)• Take output of software as is, and calculate:• ug/m3 actual = ug/m3 calculated * Pamb/Pcal * Tcal/Tamb

• Where one P and T are calibrated conditions and one P and T are ambient conditions

• But Pamb and Tamb completely drops out of calculation• Only important variables are Plens and Tlens

• Doesn’t work if mass flow entering detection and mass flow leaving lens not same• Flowrate drops out in math if all assumptions hold true

• Math in software is perfect• 2 assumptions

• Actual AB signal is exactly linearly proportional to flowrate measured in lens• Tlens does not change

• Calibrate at known T and P, convert to STP and then after measurement readjust for actual measurement of T and P under sampling conditions

• In molecular beam, supersonic expansion nonlinear w/ pressure? Need to check this

• Airplane: apply AB and flowrate corrections (correct math to get standard ug/m3) and check that it makes sense

Apply MS correction factors for all data

Mult cal implemented within autosave; should stop autosaving to put gap in data whenever modify/cal instrument

• Tune mult when down 10-20% (this AMS losing ~4% gain/day)

• Apparent RIE of NH4 can change w/ voltage, especially when putting in new mult(i.e., 3.4kV to 1.5kV)

• Sometimes mult becomes more stable at higher voltage

Load tab: ‘Invoke Corrections’ and ‘Plot Diagnostics’Set MS and TOF to default species, MS corrections, Auto Update, Graph update

Full data set loaded and corrections applied

AB and flowrate smoothing (4 pts each-40 min)

•Most of AB noise has to do w/ ion counting statistics

•Actual amt of smoothing dependent on instrument characteristics

•No appreciable change in concentrations/trends w/ smoothing

•Change colorscale to show variations

More in-depth look at data

Avg MS (5941-5993) in log and linear scale where see amsmostly measures air

• Can easily see gas-phase components (gray) and start to see particulate (colors).

• Yellow is unaccounted• Seems to be real signal at 40 (mostly argon, but may be some particulate)

• 39 is K from surface ionization-changes

• 22 not known• 31 something (should label)

• Assume 28 is all N2+ (factor of 107 to real atmosphere)

• 44 (CO2+) gas assumes 370 ppm(~50 ng/m3)

• Methane next most abundant at ~1.7ppm and is in noise

• Need to do some tweaking to get nh4 correct (m/z 17:16 should be 1.1)

• Looks like ox org (‘aged’) MS

Fragmentation Waves• Assume all of signal at m/z 28 is due to air• 29 – N15 abundance multiplied by 2• 40 – 0.9% argon, RIE argon slightly larger than N2, 1.28 is fraction of atmosphere that is

not N2 and there is some fragmentation of N2 into 14 (1.14)• 44 – mix ratio 370ppm, RIE 1.36, composition of air 1.28, frag into 14 1.14

• 3 parameters that have to be set by each user• O16 – referenced to 14 b/c assume same processes govern fragmentation of N2 to

N and O2 to O.• Gas-phase water – default is 0.01 (1% of atmosphere is water vapor-absolute), but

this is variable depending on location• Not general, but can write function to vary this parameter if have good water

measurement• Fragmentation pattern is set, empirical measurement (Ann M.)

• CO2 – 370ppm

• At any m/z, there is only one that has that m/z first (i.e., only one species is dominant for any m/z)

• Unaccounted: 22, 31 (very small nitrate contribution), 39 (K+), etc.

• Interferences btw inorganics and organics are accounted for, but there are exceptions when sulfate or organics are very high

Check m/z• Check raw spectrum, width bars, integer m/z on avg MS

window• Corrections tab: open+closed redoes m/z cal on open and

closed separately and then takes difference• Precise masses to use for m/z cal (non-integer)• Wave has non-integer value of every m/z to look for signal;

offset gets larger as increase m/z

Point CnH2nPLUS2_plusAmbient_amu10 1111 1212 13.007813 14.003114 15.023515 15.994916 17.026617 18.010618 1919 2020 2121 2222 2323 2424 2525 2626 27.036927 28.006128 29.039129 29.99830 31.041431 32.042532 33.043633 34.044734 34.968835 35.976736 37.048137 38.049238 39.050339 40.051440 41.052541 42.053742 43.054843 44.055944 45.05745 45.992946 47.0592

Recalculate m/z

• Recalculate sticks (using non-integer masses) - shifted slightly• Better to use ‘amus_alt’ wave that has slightly different m/z

values (generated from periodic table using CnHm combinations w/ few exceptions-Ar, CO2, benzene, toluene) – user definable

Point CnH2nPLUS2_plusAmbient_amuamus_alt25 26 26.035826 27.0369 27.036927 28.0061 28.006128 29.0391 29.039229 29.998 29.99830 31.0414 31.041431 32.0425 32.042532 33.0436 33.043733 34.0447 34.044834 34.9688 35.045935 35.9767 35.976736 37.0481 37.048137 38.0492 37.973738 39.0503 38.963739 40.0514 39.962440 41.0525 40.961841 42.0537 42.053742 43.0548 43.018443 44.0559 43.989844 45.057 45.057145 45.9929 45.992946 47.0592 47.059347 47.967 47.96748 49.0615 49.061649 50.0626 50.062750 51.0637 51.063851 52.0648 52.064952 53.066 53.066153 54.0671 54.067254 55.0682 55.068355 56.0693 56.069456 57.0704 57.070557 58.0715 58.071758 59.0727 59.072859 60.0738 60.073960 61.0749 61.07561 62.076 62.0761

Using CnH2n wave

Using amus_alt wave

High m/z

PAHs at non-integer masses (red)

So recalc works for large m/z too

Recalibration Results• Change from recalculating sticks: dynamic tweak w/ slope (1 if perfect) and intercept (-0.5

if perfect)• Uses linear interpolation from major signals• Big switch is when acquisition software makes change (0.05 step) during autosave, but

only changes intercept (automatic autosave procedure uses only m/z 28, now very stable)• Difference of 0.05 amu is important for edges of big peaks like H2O and can be

differences btw open and closed – recalc corrects this as well• Slope set when you do manual m/z calibration (usually m/z 28 and 149)

• Resolution (1 amu) is ratio DC voltage:RF voltage (set by quad voltages)

Error• Corrections panel: uncheck recalc sticks and check perform analysis• Avg MS: replot graph to include errors

• Bottom – electronic noise (ion counting), shouldn’t be completely flat• Top – signal• Length – s/n

• Ultimate noise level determined by particle counting statistics, so should view electronic noise as lower limit

Data DiagnosticsGives general indication of fragmentation and large-scale trends-------------------Ammonium – relative fragmentationLinear least squares fit of m/z 17 vs m/z 16 and set O16

Fragmentation and neutralization (see systematic offset in neutralization b/c of incorrect m/z 17/16 ratio

Ammonium O16 correctionSet O16 to 0.32 (from 0.335) – just about perfectNeutralization also very close to 1:1 and deviations from 1:1 are meaningful (probably particle growth event)

Sulfate – ratio to m/z 48• Ratios fall on lines – signature of (NH4)2SO4 (vaporizes mostly as SO3 + H2O• For H2SO4, m/z 81 becomes dominant and m/z 98 also high• For NH4HSO4, need high percentage to see change in fragmentation from

(NH4)2SO4

Nitrate• Line typical value (data usually higher than shown), but constant ratio indicates

NH4NO3 (qualitative picture)• If other NO3, then ratio becomes messier• Ratio can also change with vaporizer temperature• Also factor of 2 variability in laboratory NH4NO3 – not well understood• Ambient always have lower 46/30 ratio than laboratory – also not understood• Mineral nitrate has almost no m/z 46• Implies vaporization issue (more NO+ than NO2+)

OrganicsGives some indication of primary/oxidation(black dotted lines are Doug’s additions)

Mass Resolution• Look at m/z 27/28/29 b/c m/z 28 is biggest (most problematical) peak• m/z 29 can have significant particulate signal if resolution set correctly

• C2H5+, CHO+, but mostly N15 (gray) fixed based on m/z 28• m/z 29 is really convolution of N15 and organics, which have different non-

integer amus• Low/high mass resolution different

• High mass side (right) should come sharply down (leakage 10-6)• Should be small dip btw m/z 28 and 29

• Low mass side (left) has tail • Leakage is smaller (10-4)• Often small leakage from m/z 28• m/z 27 vs total organic and check intercept to see if/extent leakage

• Add to data diagnostics• Look at before/after recalc sticks

• Should be sharper after

Mass Resolution 2• Trying to make peaks be ‘top hat’ w/ dip between peaks so that resolving peaks

while retaining the largest amount of signal• m/z 14 – almost completely N• m/z 18 – all H2O+, but different (4) sources

• Shape of 18 not as smooth as others b/c difference spectrum and 18 background is very large and added signal relatively small

• Green – org H2O, set as same size as CO2+ (m/z 44)• Red – sulfate from evap of SO3+H2O, but not exact fragmentation• Gray – gas-phase (RH) set by user, currently 1 value but may be able to

change to variable wave to be more accurate• Blue – particulate water, residual (total m/z 18 signal - everything else)

• m/z 17 – OH+ and NH3+• All colors are just fraction of m/z 18 (0.27), doesn’t matter what kind of water• Orange is residual (total m/z 17 signal – everything else)

• m/z 16 – O+ and NH2+• Same case as m/z 17, except O+ correction dominates and is instrument

dependent (frag_O16 in frag list)

Create/Destroy Mass (Godwaves)• Make calculation wrong (change RH[18] 0.03 and cause negative values to appear

(black bar) • Negative appears as positive black bar so that can still see them in log scale• Negative numbers caused by:

• Noise• Bad math

• Make new panel at bottom of graph that shows negative numbers from mass calculations and add another panel to time trend that plots magnitude of negative numbers b/c inherent in all calculations that can create/destroy mass – means something isn’t being calculated correctly

• Dependencies in frag list allows this to happen

Create/Destroy Mass 2• Noise is 1 sigma and anything larger than factor of 2 is real, so look at all black

bars• m/z 65 negative: combination of SO3 isotope from 64 and estimated organic• Tungsten at m/z ~185 and m/z 149 – noisy signals that are difficult to subtract

• All organic fragmentation patterns assume a reasonably smooth trend and works pretty well for ambient, but doesn’t work for lab expts where looking at small number of molecules where pattern is very specific

• Ann – only 5 m/z where organics averaged from +/- 14 amu to account for organics at sulfate-influenced masses

• Can’t use output of James’ panel as black box, have to check to make sure all calculations done correctly by looking at noise level, negative values, etc.

Size Distributions• Make sure MS time series correct• Check ‘Normalise to MS’ and ‘Use MS correction factors’• Slightly negative baseline

• Plot Signal vs TOF (raw data) to see how baselines calculated• In data acquisition, pick time period at beginning and end for

‘zero’

Baseline Recalculation• Ammonium always has non-zero baseline b/c the gas-phase ammonia always leaks

into particulate• Gas-phase water (water vapor mixing ratio) also visible• For those masses that have gas-phase signal, only use DC markers at end (region 2)

and if have large particles use only region 1 (beginning DC marker)• Change DC

• 1200-2000 us for 1 and 2 (region 1)• 6700-8200 us for 3 and 4 (region 2)

• Signal vs TOF shifts slightly after recalculation

Region 1 Region 2

After DC marker recalculation – improves a little, but DC markers already set pretty well

Gas-phase

Some particulate signal

Boltzmannexponential distribution

‘Zero’• Definition of zero:

• Equal positive and negative numbers• Poisson distribution w/ 1 sigma translates to:

• 2/3 blanked out w/ 1/6 negatives• So 2/3 should be white and 1/3 colored evenly black/color

TOF Smoothing• Chopper 5 steps/channels wide (2% chopper and 30 us), 8 channels for 1%

chopper (10 us??)• TOF smoothing 4 pts b/c about same size as chopper width so should have small

effect on actual distribution

TOF gas/particle• Starts at 2nd DC marker, but for those species that have gas-phase contribution it

can be significant• Check ‘GP/IPP Boundary’ for each instrument

• If set this, then exclude anything before that value (in nm) from particulate calculation

Gas-phase

Integrate• Integrate – restricts to ‘particulate’ signal only (20-2000 nm) or a mode (e.g., 100-

400 nm)

Integrate button on TOF panel

General CommentsVery important to do good job of AB correction

Don’t tune ionizer in first few days after pump down because everything is changing (outgassing); wait until stable

Make gap when making change to instrument (i.e., multiplier calibration)

m/z calibration should be checked when not autosaving for awhile because only automatically checks m/z calibration when autosaving, especially before doing IE calibrations

Flowrate (Slides 8-10): calibrate baratron at known pressure and temperature and relate to STP and account for changes in ambientconditions post-analysis