Isotopident is a tool that helps you to estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Moreover, Isotopident is capable of computing its monoisotopic mass. Finally, this tool is also able to predict the most likely isotope combination and the exact mass of the given input. Please read the following to make a better use of this tool (permitted input syntax, for example).
Type of composition:
Here, it is necessary to indicate the type/form of INPUT sequence. There
are four possibilities: Protein One-letter code, Protein
Three-letter code, Bases code and Chemical formula.
By default, three significant digits will be shown in the output. The
user can change it to obtain the results with four, two, or even
one significative digit.
This field lets the user to enter (copy and paste, or upload a file) a
set of characters that corresponds to the peptide/protein, polynucleotide
or the chemical compound that is under consideration. Only one of those
ways should be used (copy-paste or file upload).
Supported data formats:
This tool only lets you to enter data that follows these rules:
More input examples:
The output page will display a filled table with a summary of the
chemical elements and their corresponding masses (average). For example, if the input is:
the corresponding output would be:
Note: the system will add one water molecule (H-NH-CH(R)-CO-OH) since the N-terminal part needs an H and the C-terminal part an OH each time the entered sequence would be a Protein. Besides, the system will indicate if an entered isotope is not defined.
The elements are shown in the following order: Cn1 Hn2 Nn3 On4 Sn5...
On the other hand, the program plots an interactive 2D graphic showing the theoretical isotopic distribution of the entered sequence. For example, the theoretical isotopic distribution for the previous entered peptide would be:
Zooming in and out is supported. To zoom in, drag the mouse downwards to draw a box. To zoom out, drag the mouse upward. If you zoom in far enough, the plot becomes unreliable. In particular, if the total extent of the plot is more than 232 times extent of the visible area, quantization errors can result in displaying points or lines. Note that 232 is over 4 billion.
A text file with the plotted points can be downloaded. This file has two columns after some plot related data: mass in Daltons and Intensity that correspond to the axes X and Y respectively. For the previous example, this flat file would be:
TitleText: Isotopic distribution
YLabel: Intensity ( x 100)
Besides, the system will show the following information:
Most likely isotope combination:
The system calculates the most likely combination of isotopes fitting the given formula. And, the probability of this combination is calculated. This can be useful if a high precision mass is wanted. If the combination is the dominant contributor to the response at a particular integer mass, then it should be readily measured on an accurate MS.
Exact mass is 9010.402
Probability of combination is 7.595%
The most likely combination is 52.91% of those masses rounding to 9006 amu.
The system only computes the exact mass for the input when the entered sequence (Chemical formula) in the molecular composition field has been written using one or more specific isotope for a given element. On the contrary, the average mass is computed when the input has no specific isotopes. For example, if the entered sequence is:
Then, the system will only find out the exact mass as follows:
Note that in case that the user enters an isotope that is not defined, the system will show a message indicating that this one is not a stable isotope. For instance, in the previous example the O is not a stable isotope.
Finally, if the entered sequence in the molecular composition field is invalid, the system will display a message telling which one(s) is(are) the unrecognized character(s) painting it(them) red. In this case, please check also if you have selected the right Type of composition.
Notes and definitions:
You can also see some notes about the MS Identification process.
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