IBG Maldi Quantifier User Documentation

The IBG Maldi Quantifier tool is for quantifying the degree of modification in Maldi mass spectra. It was developed around the modifications of phosphorylation and thiophosphorylation. The tool reads in two user provided spectra, the Linear Positive spectrum and the Linear Negative spectrum. It searches for the peak represented by user defined peptide mass in both spectra and then searches for the modified peak which is the peptide mass + modification distance. When the peaks are discovered, the relative percents of the unmodified peak and modified peak are computed for both spectrum. The modified peak percents are then averaged to obtain an accurate percent figure of the modified peptide.

User Parameters:

Linear Positive file is the MS1 MALDI spectrum in linear positive mode which contains data from an experiment on modified peptides.

Linear Negative file is the MS1 MALDI spectrum in linear negative mode which contains data from an experiment on modified peptides.

Zip file is a zipped file containing multiple pairs of MS1 MALDI spectra. This parameter is specific to IBG Maldi Quantifier (zip). This interface was developed because of lack of mzXML support and retreival of relative meta-data from MALDI machines. Some naming constraints on the zip files are:

• All files must be named in the form XXX[0-9].pos.xxx or XXX[0-9].neg.xxx where the XXX of the pos equals the XXX of the negative to make them a pair.

   Example: D1_LINEAR_2.pos.txt and D1_LINEAR_3.neg.txt are considered a pair.

• All files must be in a directory named in the form [SEQUENCE]_mz_[PEPTIDE MASS] .

   Example: ADAQHATPPKKKRKVEDPKDF_mz_2407

• The directory must be zipped and the extension is .zip .

   Example: ADAQHATPPKKKRKVEDPKDF_mz_2407.zip

Peptide Mass is the mass of the peptide to be quantified.

   Example: 2407.0

Modification Distance is the mass of the modification, ie. the distance between mass of the unmodified and modified peptide peak.

   Example: 80.0

Linear Positive accuracy figure and Linear Negative accuracy figure are the values of how accurate your spectra are. These value are used when evaluating whether a peak near the mass of the peptide is in fact the peptide peak.

   Example: 1.0

Combine Peaks Range is used to combine peaks within a certain range around the peptide peak. This is used when a spectrum is mis-interpreted by the peak detection software and resolves the peptide peak into several peaks. This maybe deprecated soon.

   Example: 4.0

Output:

There are two forms of output.

• The first is what is displayed on the main page and is in form of

Linear Postive percent: [modified percent]%
Linear Negative percent: [modified percent]%
Average percent: [average modified percent]%

LINEAR_POS: [unmodified]([mass/charge], [intensity]) = [unmodified]% [modified]([mass/charge], [intensity]) = [modified]%
    MassError: [input modification - actual modification]
LINEAR_NEG: [unmodified]([mass/charge], [intensity]) = [unmodified]% [modified]([mass/charge], [intensity]) = [modified]%
    MassError: [input modification - actual modification]

Total Intensity: [sum of peak intensities]

   Example:

Linear Postive percent: 72.52%
Linear Negative percent: 73.89%
Average percent: 73.21%

LINEAR_POS: (2417.8941, 0.379) = 27.4816% (2498.0509, 1.0) = 72.5184%
    MassError: 0.1568
LINEAR_NEG: (2415.9337, 0.3533) = 26.1064% (2496.0128, 1.0) = 73.8936%
    MassError: 0.0791

Total Intensity: 2.7323

• The second form of output is a comma delimited file which may be obtained by the link labeled Export CSV Results on the results page. An example results file may be downloaded here: ExampleResults.csv.

NB -The CSV export file was reformatted (Oct 2006) to produce a columnar result listing the following parameters:

Archive. Mode, Percent, Average Percent, File, Total Intensity,Pa M/Z,Pa Intensity,Pa Relative Intensity,Pb M/Z, Pb Intensity, Pb Relative Intensity, MassError, Peptide mass, Modification Distance, Linear Positive Accuracy Figure, Linear Negative Accuracy Figure, Combine Peaks Range

• AADAQHATPPKKKRKVEDPKDF_mz_2408.csv: Here's a CSV export from a typical MALDI experiment using the updated CSV export format (above).

-- LarryHelseth - 27 Jun 2007
-- KevinDrew - 21 Apr 2006