Maldi PTM Quantifier

Tool for quantifying degree of modification in Maldi mass spectra, designed around phosphorylation and thiophosphorylation

* overall strategy, coming from our observations on relative intensities in positive and negative modes:

note how the average of ratios observed in the two modes is closer to the actual ratio input in the sample (with error "+/- n%")

TimeLine

Requirements for accurate analysis:

• Replicate analysis--calculating average and standard deviation for three separate spot replicates in each mode (kdrew: 1.5 weeks)

• Averaging two modes--calculating averages of the replicate averages from the two modes and assessing error as "+/- n%" (kdrew: 1 week)

• Ability to compare more than one sample: i.e. plot "calibration curve" of apparent ratio results from numerous known concentration samples (kdrew: 3-4 weeks)

• OPTIONAL place to enter in "Known concentration" to allow for analysis of how accurate the averaging of the ratios from the two modes was (kdrew: 1 week)

Output from analysis:

• Table with entries for: average %Pb-pos mode from replicates; std. dev. for %Pb-pos mode from replicates; average %Pb-neg mode from replicates; std. dev. for %Pb-neg mode from replicates; avg. of avg. from each mode; error "+/- n%" for this average (kdrew: 1 week)

Helpful features to build in:

• Ability to upload multiple data files at once and subsequently create groups of replicate spectra--these experiments will generate many spectra of various ratios. High throughput analysis will be essential, and allow us to create data handling structures that will be useful for future modules. (kdrew: depending on Kah ~6-10 weeks)

• Ability to define Pa m/z and Pb m/z (or modification distance)--these experiments will usually use known peptides of known m/z and only need to find relative intensities (as isotope cluster area) for set Pa/Pb pairs. (kdrew: 1.5 weeks)

• Ability to define and analyze more than one Pa/Pb pair per spectrum--this will allow for multiplexing the experiment, i.e. adding peptides of different mass in the same MALDI spot and looking at their degrees of phosphorylation. (kdrew: 2-3 weeks)

Total: 1.5 + 1 + 4 + 1 + 1 + 10 + 1.5 + 3 = 23 weeks (kdrew: this tries to include design, development, prototyping, bug fixing, redesign and new feature/feedback requests. Some of this time is overlapping but some are prerequisites of others.)

• 84phos-linearnegativerep1.txt: sample file

• 84phos-linearnegativerep2.txt: sample file

• 84phos-linearnegativerep3.txt: sample file

• 84phos-linearpositiverep1.txt: sample file

• 84phos-linearpositiverep2.txt: sample file

• 84phos-linearpositiverep3.txt: sample file