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Metastables is a software module to select the correct atom or molecule for gas phase experiments. The file includes a list of 60000 metastable species. For each species the software will calculate the exact mass of the molecule and detect ions that can be formed. Metastables will then calculate the expected first ion of fragmentation and the position of the peak in the mass spectrum. Using the calculated data the user can select the appropriate ion pair to carry out the gas-phase fragmentation experiment.

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GATA-6 is a zinc-finger transcription factor that mediates many biological processes such as cell cycle regulation, cell differentiation and apoptosis. After a GATA-6 nuclear translocation, it binds to a specific DNA sequence (GATA binding site), thereby modulating target gene transcription. GATA-6 is a master regulator for blood-forming stem cells to maintain the GATA-6 levels in proper range is essential. Since patients with GATA-6 deficiency have very low GATA-6 levels in their blood cells, a new method is now possible to diagnose if patients have GATA-6 deficiency. It is hoped that this method will help to prognosticate and predict the outcome of patients suffering from blood loss.
The protocol requires the procedure to detect GATA-6 protein expression in biopsy tissues of patients with hematologic disorders. The specific steps include:
1. Remove biopsy tissue of the patient
2. Fix in formalin solution until time of processing
3. Prepare formalin-fixed paraffin-embedded (FFPE) tissue into tissue blocks for preparing paraffin sections and putting it into a specialized machine for generating paraffin-embedded sections
4. Block endogenous peroxidase activity by incubating FFPE tissue sections for 20 minutes in a 30ml of 3% hydrogen peroxide solution
5. Wash and rinse sections with PBS
6. Cut the paraffin-embedded sections into 3mm thick sections
7. Gently transfer the sections to a slide which is placed in a staining box
8. Incubate the sections in 100ml PBS containing 1% BSA, 0.1% NaN3 and 0.1%

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Mean Mass: The average mass of ions that are created during low (0.1) collision energy
collisions of the ions. This parameter is very close to the mass/charge ratio of the original molecules of the metastable ions. The difference is usually less than 0.1%
of the ion’s mass.
Molecular Mass: The exact mass of the molecule you are trying to create.
This is a list of metastable ions. To find the exact mass, you need to add the molecular mass together with the mean mass. If you want to determine the exact mass, you need to replace the mean mass in the equation with the molecular mass
and then check the ion you are looking for.
Ion Mass: The exact mass of the ion you are trying to create. If you only want to determine the molecular mass, you only need to replace the mean mass with the molecular mass.

The Open Source version of Metastables is released under the GPL v3 license.
Versions of Metastables available for download

Metastables_v1.01.zip v1.01 containing a basic version of Metastables (see below). This first version provides several checks for the required values, but you have to fill them manually.
Metastables_v2.01.zip v2.01 is an improved version of Metastables with a graphical user interface (GUI).
The interface is able to calculate the mean mass, molecular mass and/or molecular ion mass values of metastable ions (see below). For this version you need to select ion-pairs for each case with a GUI.
When you want to get the molecular mass using the mean mass you need to input “the exact mass of the molecule you are trying to create. If you want to determine the exact mass, you need to replace the mean mass in the equation with the molecular mass.

Metastable Values

Metastables is able to calculate the molecular mass and the mean mass for metastable ions. Therefore, you need to fill the boxes below with information about the molecule you are trying to create.

The molecule you are trying to create needs to be stored as a standard molecule (without protons or deutons). More information about standard and neutral molecules are available in the MS-help

The molecule you are trying to create must exist in the database in an entry with a molecular mass that is between 100 Da and 300000

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Metastable mass spectra originate from metastable decay in the source field after acceleration. Usually the metastable ions are in a relative motion. This motion leads to random losses in their specific energies and spreads the peaks in the mass spectrum out in a background spectrum.

Reference Material:


In short, no.
There is not a single mass on the spectrum where the deuterium and the tritium have exactly the same mass to within 0.1 or 0.01 or even 10%. That doesn’t mean there is no relationship or correlation, but there is no singular point.
Also remember that the error estimates are estimates based on the statistical nature of the measurement. Perhaps there is a big difference where the actual error gets capped at around 0.1 because of jitter, but you are likely to have more like 1-10% error in your actual peak locations.
A simple example of where there isn’t a standard for this: In a sample where the tritium is treated in a different way from the deuterium. Do they get similar spots on the mass spectrum? Not necessarily.
In fact, the big problem is that this relationship is highly dependent on your instrument. What are the resolving powers of the different peaks? What is the error you get on the measurements? What is your data acquisition method? All of those can impact the results.
To address your question a little more directly, yes, generally there is a relationship. But don’t get too hung up on it. You have to understand that it is actually quite variable and there are multiple ways to get it.
Another thing is that all of these mass spectrometers are sophisticated scientific instruments and they are highly tuned to some specific standards. As such, you are going to have a certain baseline and how that relates to your ionization source is going to vary a bit.
I’m going to take a step back here.

Just to list a few things that all mass spectrometers will have:

A magnetic field
Resolving power
A mass filter
A collision cell (gas, liquid, or sometimes solid)
A drift tube
Some way of accelerating ions
Spectrum acquisition and display hardware

I’m going to skip most of the details. I’m going to assume you have the magnets and filters. This is where the calibration of the spectrometer will start to differ a

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Minimum mass is the required mass of the metastable ions (M*) that need to be mass analyzed. All ions with a lower or equal mass to the minimum mass must be ignored. The reason is that the cooled trap still has not enough kinetic energy to break the metastable molecule and that the ion mobility spectrometer will not provide any information about the desired ions.
Maximum mass is the mass of the metastable ions (M*) that you are looking for. The ions should have their maximum possible size to obtain the desired fragmentation.
Accuracy should be as high as possible. Calculating the exact values will lead to more information about the molecules in the spectra.
Does anybody know how to calculate the above defined compounds? I guess that there are some equation for that. But I don’t really know where to look for them in the literature.
Thanks for your help.


If I understand the question correctly, the following formula is what you’re looking for.

$\frac{M*}{M1} = (M2*M2)/M1$

as detailed in the paper “Differentiation of Metastable Ions in a Magnetic Trap” by Sood and Lauda.
To confirm this, I did a little calculation on the Metastable plugin for Skyline. The plugin describes how it uses a Metastable Explorer to determine the parent masses and hence, the measured metastable masses.

// detail/null_event.hpp
// ~~~~~~~~~~~~~~~~~~~~~~
// Copyright (c) 2003-2017 Christopher M. Kohlhoff (chris at kohlhoff dot com)
// Distributed under the Boost Software License, Version 1.0. (See accompanying
// file LICENSE_1_0.txt or copy at


#if defined(_MSC_VER) && (_MSC_VER >= 1200)
# pragma once
#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)



System Requirements For Metastable:

Recommended System Requirements:
Minimum specifications:
OS: Windows XP/Windows 7/Windows 8/Windows 10
Processor: 1.8 GHz Dual Core Intel CPU or equivalent
Memory: 512 MB RAM
DirectX: Version 9.0 compatible graphics card (2 GB VRAM)
Hard Disk: 5 GB available space
– Wii U GamePad
– A USB Mass Storage Device (SD card recommended)


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