Introducing.. PIKA (Ochotona princeps)

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1 Introducing.. PIKA (Ochotona princeps) Pikas are hearty little mammals who live in rock piles high in the mountains of western North America. PIKA, or Peak Integration by Key Analysis is a software tool for High Resolution AMS analysis. 1

2 Peak Integration by Key Analysis (PIKA) First Steps Brains: Peter, Allison, Marc, Jose A few more Brains: Manjula, Jesse, Tim, Dara, Qi, John, Doug, et al Coding Muscle: Donna et al 2007 AMS Users Mtg, Reno/Sparks, NV Issue: In v and w mode ToF data we often see tantalizing multiple peaks at integer m/z. Random example: m/z CH 2 O 13 CHO Difference, Hz Difference, Hz NO C 13 CH 5 CH 4 N C 2 H m/z m/z Goal: Apportion signal to all contributing ions, be as quantitative as possible. (Do this for many spectra.) 2

3 Goal: Apportion signal to all contributing masses, be quantitative What is needed for this analysis? Have a good m/z calibration Know all possible masses from EI Method for selecting masses to fit Know (isolated) mass peak width as a function of m/z Know peak shape Difference, Hz CH 2 O 13 CHO NO m/z C 13 CH 5 CH 4 N C 2 H What tools do we already have? Squirrel framework for accessing data sets Unit resolution (aggregate) values for comparison Good m/z calibration routine What new tools will we need? Big table of all masses, mechanism for choosing which masses to fit Mechanism for deriving parameters of peaks Diagnostic plots, etc. PIKA Analysis Flow Chart SQUIRREL HDF Index Tab Get Index squirrel index Pre-Process 0A 0C integrated species (Hz) raw spectra open, closed (Hz) Check m/z calibration m/z parameters 0B SQ step 0A. Get organized SQ step 0B. Good m/z parameters SQ step 0C. Raw open, closed PIKA Set Up HR Fits Tab Calc and View HR Fits Tab Create Raw Diff Spectra integrated species (Hz) raw spectra diff (Hz) Peak Width, Shape peak width, shape parameters Calc HR Sticks for One Run HR peak heights HR Unit Spectra 1 2 HR Sticks Plot Choose Masses to Fit Exact Mass waves 4 HR Unit Residuals Spectra Raw diff spectra 2. Peak width, shape 3. Choose masses to fit 4. View graph for one spectra 5. Repeat 3,4 6. Fit many runs. Calc HR Sticks for ToDo Exact Mass waves HR masses vs time HR residuals vs time 6 3

4 SQ step 0A. Get organized SQ step 0B. Good m/z parameters SQ step 0C. Raw open, closed 1. Raw diff spectra (no plot) 2. Peak width, shape (big panel) 3. Choose masses to fit (little panel) 2. Peak width, shape View peak width for many runs. View peak shape for many runs. or masses Select masses for fit View fit for one run Only a few parameters are used in proceeding step! Peak width slope & intercept and Peak shape 4

5 3. Choose masses to fit Subset of selected chosen masses that are isotopes. In the Isotope Mask column set values to 1 (constrain) or 0 to vary from isotopic parent. Table of all known masses. In the HR Mask column set values to 1 (fit) or 0 (no fit). 4. View graph for one spectra 5. View residual plots, comparison with Squirrel unit sticks, etc Repeat 3,4 as needed. 6. Fit many runs. View residual plots, time series, etc 5

6 Parting words Start with a small data set! Code is not yet optimized for speed. Do not presume that the default selection of masses will work! Code does not yet do final conversion to µg/m3. Be on the look-out for a PIKA web site. There will likely be many new releases in the coming year. Tell all about additions, corrections to exact mass all table. Be aware of PIKA color scheme for CH, CHO, etc families. Tell me of problems, must-have features. 6