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Tarskin / LaCyTools

A high-throughput data extraction package for LC-MS data.
Apache License 2.0
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Isotopic pattern relative intensities give nonsensical values in the analyte.ref for intact protein fragments ca. 25 kDa #31

Closed DhunShafir closed 6 years ago

DhunShafir commented 6 years ago

I was trying to calculate the isotopic patterns of a protein fragment (ca. 25 kDa).

While it looks like I am getting the correct masses of the most abundant isotopes, the relative intensity is nonsensical (see attached analytes.ref).

For example, m/z 1190.30 should be the most abundant isotope according to "http://www.envipat.eawag.ch/index.php", which matches the fact that 1190.30 is also the middle isotope calculated by LaCyTools (at this size a Gaussian-like distribution around the most abundant isotope is logical).

I also attached the LaCyTools script I ran, in case I added the error when I added the building block.

Issue 180406.zip

Tarskin commented 6 years ago

This issue does not appear when using the Isotopic Pattern calculator (as supplied with MassyTools).

Tarskin commented 6 years ago

LaCyTools correctly calculates the isotopic pattern for 8 IgG1 molecules, but at 9 IgG1 (>10 kDa) molecules the pattern goes wrong.

analytes 7 IgG1.txt analytes 9 IgG1.txt analytes 8 IgG1.txt analytes 3 IgG1.txt analytes 5 IgG1.txt

Tarskin commented 6 years ago

This bug will be closed once the fix has been verified by two separate users.

Tarskin commented 6 years ago

This fix has been verified by Guinevere SM Kammeijer.

Tarskin commented 6 years ago

This bug will be closed as the fix has been verified by several sources.