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PIKA: Overview & best practices
Delphine Farmer+ Donna S, Tim O, Mike Q,…
2009 AMS User’s Meeting
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
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Step 0. Set up in Squirrel (m/z cals, baseline, etc.)Step 1. Raw spectraStep 2. Peak width/shapeStep 3. Choose HR masses to fit
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
• Subsample with to-do wave
• New default list (Puneet)• in general, start with small list and then expand, p ,otherwise you’ll get spurious peaks…
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
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You almost always improve your residuals by adding more peaks… but maybe hides peak shape/width problems?
• fits are low between CHO & CH peaks • add in CHN2 & CHN
In this case, Ar+ looks good, but not good enough…
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In this case, Ar+ looks good, but not good enough…
Use the residuals to find problems
‘wings’ = peak width
Residual Diagnosis
‘sine’ = m/z cal
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You almost always improve your residuals by adding more peaks… but maybe hides peak shape/width problems?
• fits are low between CHO & CH peaks • add in CHN2 & CHN
Recommendation: avoid CxHyNp, CxHyNpOz and CxHyO3+ peaks unless they are clearly resolved in PIKA.
Start with fewer ions, add in…
Recommendation: avoid CxHyNp, CxHyNpOz and CxHyO3+ peaks unless they are clearly resolved in PIKA.
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Sandwiching: small peaks between 2 large peaks that get fit, but aren’t necessarily there
→ CxHyNp+, also some CxHyOz>3
→ minor effect on CH/CHO/NO, but huge effect on CHN family→ minor on O/C, H/C, potentially impt to N/C
Sandwiches are people-food, not PIKA-food
check every CHON ion
Or use the default list instead
Calc HR sticks
Remember: bad things can happen when you blindly fit peaks in PIKA… the extreme changed our
CHN/CHON families from 5-20%…
{Velociraptors are dangerous to PIKA’s health: think critically and proceed with caution…}
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Real Spurious
• Key ions (Ar+, N2+, CO2
+) have perfect m/z, peak shape
• Residuals shouldn’t have
• Key ions (Ar+, N2+, CO2
+) have residual problems
• Be suspicious of adding tooResiduals shouldn t have ‘wings’ (peak shape) or sine shape (m/z cal)
• If residuals only marginally improve, probably not worth it (?)
Be suspicious of adding too many sandwiched peaks
Should I look at every ion???Should I look at every ion???
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Non-fit peaks
• you wouldn’t know unless you looked at every peak OR Step4 Print All Errors To History
Non-fit peaks
• residuals….
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SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
Should I look at every ion???
PIKA is an iterative process
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Plot open vs. closed cal for your dataset and see
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
for your dataset and see if there’s a difference…
Quick look to look at ion choices, peak fits
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
Vs.
ALWAYS before diagnostics, etc.
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Plot open vs. closed cal for your dataset and see
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
for your dataset and see if there’s a difference…
Diagnostics…
• look for anything abnormal
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• look for anything abnormal, error bars on ions useful; check CHON, CHN, CS peaks to see if
USE the diagnostics!
Diagnostics
they’re “real”
Diagnostics…
SetUp HRFits | HRFits 1 Spectra | HRFits Many Runs | HR Results
Again, you’re looking for anything g y gdifferent, peaks that don’t fit a pattern…
• Always have to reiterate between Fits for One spectra/Many runs with Peak Shape/Width, m/z cal…
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Final Caveat: look at ions before interpreting them…
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Summary
• PIKA is an iterative process:• Careful adding spurious ions vs. peak shape/cals/etc.• Watch for sandwiched peaks• Use the diagnostics & residuals• look at ions before interpreting themlook at ions before interpreting them…
http://cires.colorado.edu/jimenez-group/wiki/index.php/High_Resolution_ToF-AMS_Analysis_Guide
Or… J-Group Webpage → ToF-AMS wiki → HR Analysis guide