.. seealso:: If you wonder how to make the most out of IsoCor, have a look at the :ref:`Tutorials`.
If you don't fully understand why you should correct your MS isotopic data, we invite you to have a look at Midani et al. 2017 excellent review.
Finally, practical examples are provided in the :ref:`Tutorials`.
You will find scripts for correction of HRMS data out there, but we won’t recommend any since, to the best of our knowledge, they implement algorithms that partly fail for high-resolution datasets (see IsoCor v2 publication).
Tool | Has GUI? | MS resolution? | Tracers? | Reference | Comment |
---|---|---|---|---|---|
AccuCor | No | All | 2H, 13C, 15N | Su et al. 2017 | Faulty at High-resolution |
PyNAC | No | UltraHigh only | 2H, 13C, 15N | Carreer et al. 2013 | none |
IsoCorrectoR | No | Low & UltraHigh only | All | Heinrich et al. 2018 | none |
ElemCor | Yes | All | 2H, 13C, 15N, 18O, 34S | Du et al. 2019 | Faulty at High-resolution |
IsoCor v1 | Yes | Low only | All | Millard et al. 2012 | none |
IsoCor v2 | Yes | All | All | Millard et al. 2019 | none |
Note
If you would like your software to appear in this list, please get in touch with us.
For a compound with n atoms of the tracer element, you should measure n+1 peaks.
For a compound with n atoms of the tracer element, you should measure the :ref:`mass fractions <mass fractions>` corresponding to the compound having incorporated 0, 1, ..., n isotopic tracers.
Mass fractions cannot be corrected by IsoCor in case of missing measurement(s).
For instance, in a C2 compound for which M2 is not measured, one cannot estimate the contribution of the corresponding isotopologue – through (im)purity of the isotopic tracer – to M1 or M0. Hence, these mass fractions cannot be corrected for purity. As another example, in a C3 compound for which M2 is not measured, one cannot estimate its contribution – through natural abundance – to M3. Here again, these mass fractions cannot be corrected for natural abundance of isotopes.
To avoid misinterpretation of partially corrected data, we have prefered to not allow correction to be applied in case of missing values.
Open the relevant database file with a rustic text editor (e.g. Notepad++) and add a new row in your file following the format described in :ref:`Input data`.
Database files are created by default at the first run of isocor in '/user/isocordb'. Additional metabolites and derivatives databases can also be defined, as described in :ref:`Input data`.
Take care not to modify the file format, nor its structure. A typical error comes from Excel replacing '.' to ',' in floats.
Obviously, errors in elemental formulas will result in erroneous :ref:`isotopologue distributions <isotopologue distribution>`; thus special care must be taken when defining these formulas. Details on the elemental formulas to be declared in IsoCor can be found in :ref:`Tutorial section on formulas <formulas>`.
Yes, IsoCor takes into account the charge when constructing the correction matrix. The charge state of each metabolite should be declared in the corresponding database file, as detailed in :ref:`Input data`.
The abundance of each isotope in natural samples depends on their origin. For instance, marine organisms have been reported to have slightly less 13C than land plants [IUPAC2016]. Ideally, you should measure the exact abundance of each isotope present in an unlabeled sample prior to the labeling experiment. However, most of the time such an experiment would require too much resources for a negligible gain in precision, as we previously found [Millard2014]. The default values should be good enough for most users, unless you work with strongly exotic material.
From IUPAC [IUPAC2016].
Yes, if you know it. The purity of your tracer should be available from your provider of labeled compound.
.. seealso:: :ref:`Isotopic purity and natural abundance of the tracer`
By default, we assume a perfect tracer purity.
Yes, you should correct for the presence of isotopes at natural abundance in unlabeled positions of non-uniformally labeled nutrients.
.. seealso:: :ref:`Isotopic purity and natural abundance of the tracer`
Please have a look at the examples in the Tutorials section. If you are looking for something more detailed, we invite you to review our source code from our git repository. Also, have a look at the logs in Verbose logs mode; all the intermediate results (correction vector used to construct the correction matrix, correction matrix, etc) will allow you to reproduce the results with pen and paper.
The mean isotopic enrichment of a metabolite refers to the mean content in isotopic tracer in the metabolite, expressed as the relative fraction of total atoms of its element in the metabolite. This information is particularly useful for the quantification of split ratios between two metabolic pathways resulting in different content of tracer. IsoCor calculates the mean enrichment (ME) using the formula ME = \frac{\sum^{n}_{i=1}M_{i}.i}{n}, where M_{i} is the proportion of isotopologues with i 13C atoms for a metabolite containing n carbon atoms.
The IUPAC International Chemical Identifier (InChI) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web.
The identifiers describe chemical substances in terms of layers of information. IsoCor generates an isotopic layer that specifies the isotopologue of the tracer element, following the extended representation proposed by the InChI Isotopologue and Isotopomer Development Team:
Simple definition: /a(Ee#<+|->#...)
Complete definition:
/a(<element><isotope_count><isotope_designation>[,<atom_number>])
- <element> - one or two letter Element code (Ee).
- <isotope_count> - number of atoms with the designated isotope (#).
- <isotope_designation> - isotope designation indicated by a sign (+ or -) and number indicating the unit mass difference from the rounded average atomic mass of the element. For example, the average atomic mass of Sn (118.710) is rounded to 119. We specify two 118Sn atoms as “/a(Sn2-1)”.
- Examples:
13C2-isotopologue of alpha-D-glucopyranose:
"InChI=1/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1/a(C2+1),(C4+0)"
16O118O3-isotopologue of fumarate:
"InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/p-2/b2-1+/a(O3+2),(O1+0)"
Warning
This is an experimental feature: isotopic inchis may be subject to change according to the evolution of the IUPAC specifications.
If you installed IsoCor following our standard procedure and that you are unable to start IsoCor by opening a terminal and typing :samp:`isocor`, then there is indeed something wrong. Do not panic, we are here to help! Please follow this simple procedure:
- The first step of the debugging process will be to get a traceback, i.e.
a message telling us what is actually going wrong:
- On Unix-based systems, you should already see it in the terminal you opened.
- On Windows, you will have to open IsoCor from your Anaconda prompt with :samp:`python.exe -m isocor` to display the traceback.
- Read the traceback and try to understand what is going wrong:
- If it is related to your system or your Python installation, you will need to ask some help from your local system administrator or your IT department so they could guide you toward a clean installation. Tell them that you wanted "to use the graphical user interface of IsoCor, a Python 3.5 software" and what you did so far (installation), give them the traceback and a link toward the documentation. They should know what to do.
- If you believe the problem is in IsoCor or that your local system administrator told you so, then you probably have found a bug! We would greatly appreciate if you could open a new issue on our issue tracker. One of the developers will help you.
We would be glad to improve IsoCor. Please get in touch with us so we could discuss your problem.
[IUPAC2016] | (1, 2) Isotope-abundance variations and atomic weights of selected elements: 2016 (IUPAC Technical Report) https://doi.org/10.1515/pac-2016-0302 |
[Millard2014] | Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns, 2014, Anal. Chem., 86(20):10288-10295, https://doi.org/10.1021/ac502490g |