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Decomp Manual

If you have not done so, please read the introduction to know what Decomp is about.

Contents

  1. Overview
  2. Masses
  3. Alphabet
  4. Constraints
  5. Modifications
  6. Output and Filtering

Overview

Decomp's submission form is split into five areas. They are:

  • Masses: What are the masses of the molecules you want to decompose?
  • Alphabet: Into what components do you want to decompose them? We call this the weighted alphabet (and just say alphabet from here on).
  • Constraints: Is there anything known about the molecules?
  • Modification: What posttranslational modifications are there?
  • Output and Filtering: How should the output be presented?
Decomp needs to know at least the masses and the alphabet (corresponding to the first two areas of the submission form). The three remaining areas are optional.

Masses

Type in the masses you want to decompose. If you have more than one mass, leave a space in between. Example:

2053.3 2247.5 4525.7
If multiple masses are given, each of them is decomposed separately.

Please note: When using an amino acid alphabet, only masses up to approximately 1600 Da can be decomposed in reasonable time! (Using an allowed mass error of 0.1 Da. Using a lower mass error, larger masses can be decomposed). If the computation takes too long (> 1 Minute), it will be cancelled.

Another possibility to provide input masses is by uploading a file from your computer. The following table shows which file formats are supported and which file extensions are used to recognize them.

Format File extensions
Sequest .dta, .DTA
Micromass .pkl, .PKL
Mascot Generic Format .mgf, .MGF
mzData .mzData, .mzdata, .MZDATA, .xml
mzXML .mzXML, .mzxml, .MZXML
Plain Text .txt
Text as comma-separated values .csv, .CSV

The next option lets you select whether your input molecules have a monoisotopic or average isotopic mass distribution. This does not influence how your input masses are interpreted, but changes which alphabet is chosen and also how modifications are calculated.

The allowed mass error gives a tolerance for the mass of the resulting decompositions. If, for example, your input mass is 2053.3 Da and the allowed mass error is set to 0.1 Da (absolute), then all decompositions with mass at least 2053.2 Da and at most 2053.4 Da will be computed. If any of the filtering options are enabled, not all of them will be output, however.

The last option in this area is the computational precision, which determines how Decomp rounds real-valued masses to integers. This is necessary since the decomposition algorithm that Decomp uses works for integers. For example, if an input or alphabet mass is 1362.3418 Da, while the precision is set to 0.01 Da, then the resulting integer mass will be 136234. Because Decomp determines this setting automatically, you usually do not have to worry about it.

Note that Decomp compensates for the errors introduced by rounding.

Alphabet

The alphabet or, more precisely, the weighted alphabet tells Decomp into which constituents it should decompose the given masses. Some useful alphabets are predefined.

  • Select Nucleotides to decompose DNA molecules into nucleotides.
  • Select Amino acids to decompose proteins or peptides into amino acids.
  • Select Atoms to decompose (organic) molecules into H, C, N, O, P, and S.
For each of the three predefined alphabets, one version with a monoisotopic and one version with an average isotopic mass distribution exist. Which alphabet is chosen depends on the setting for the mass distribution. If Javascript is enabled and a predefined alphabet is selected, the correct alphabet is shown in the input field for custom alphabets. To input a custom alphabet based on this predefined alphabet, simply modify it in the text field.

Nucleotides

The nucleotide alphabet consists of the four nucleotides Adenine, Cytosine, Guanine, and Thymine.

Amino Acids

The amino acid alphabet consists of 19 amino acids. Isoleucin, which has the same mass as leucin, is not included.

Atoms

The atom alphabet consists of the six elements Hydrogen, Carbon, Nitrogen, Oxygen, Phosporus, and Sulfur.

Custom Alphabets

When JavaScript is enabled, look at the input field for custom alphabets. When writing your own custom alphabet, follow the given schema. More precisely, an alphabet is a text file in which an alphabet character is defined in each line like this:
name mass
The name may be any sequence of letters, digits, and symbols, but it should not start or end with a digit. If it does, you will not get an error message, but you may get problems reading the results. The mass must be a positive real number, possibly in scientific notation. For example, 23, 42.89, 1e-5 and 2.3e7 are valid, but -7.3 and 0.0 are not. Name and mass must be separated by space or tab. If a line starts with a #, then the line is interpreted as a comment and ignored. Empty lines are also ignored.

If you want to upload an alphabet file, it must be prepared following the same rules as above.

Example (this is one of the predefined alphabets):

# nucleotide masses, monoisotopic distribution
A 313.0576050
C 289.0463716
G 329.0525197
T 304.0460373

Constraints

If you know some constraints about the molecules you want to decompose, you can use this option to show only the relevant results. For example, if you know, when decomposing DNA, that there must be at least four Adenines, but at most six Cytosines, type A4 into the text field next to "Decomposition must contain at least" and type C6 into the field next to "Decomposition must contain at most". Multiple constraints can also be given, separated by space.

If you want to use this, the names for your alphabet characters can only contain the following characters:

  • A through Z
  • a through z
  • 0 through 9 (but a name must not end with a number)
  • the special character ' (single quotation mark)

Modifications

Three types of modifications can be used. First, mass modifications concerning the entire molecule, then, for the amino acid alphabet, fixed and variable modifications. In the two latter selectors, multiple selections are allowed, just hold down the Ctrl key while clicking on an item to select or deselect it.

Modifications of the Entire Molecule

Select a modification of the entire molecule here. The effect is that, before decomposition, the modification is 'undone' by either subtracting or adding the appropriate mass to or from the input mass.

Fixed Modifications

If a fixed modification is selected, it is assumed that all amino acids of the given type have been modified. For example, if "Acetylation (M, +42 Da)" has been selected, then the decomposition algorithm will assume that all Methionines (M) have been acetylated. Internally, this is accomplished by changing the alphabet such that the mass of a Methionine is increased by 42 Da.

Variable Modifications

If a variable modification is selected, it is assumed that some amino acids of the given type have been modified. This includes the special cases that none or all have been modified. For example, if "Methylation (H, +14 Da)" has been selected, then the decomposition algorithm will assume that all Histidines occurring in the decomposition may be methylated or not. Internally, this is accomplished by adding another Histidine (called H') to the alphabet that has a mass which is 14 Da greater than the mass of the regular Histidine. In the output, regular and modified versions can be distinguished since modified Histidines have a ' symbol appended whereas regular ones appear normally.

Output and Filtering

Show only chemically plausible decompositions

If this option is selected, a variant of the SENIOR rule is used to filter out those decompositions that are chemically implausible.

Let S be the the sum of valences of all atoms in the decomposition and n be the number of atoms. The two conditions are (from Kind and Fiehn):

  • S must be even.
  • S≥ 2n-2

Decomp knows valences for all of the atoms in the predefined alphabet (CHNOPS). In addition, it knows the valences of Na, K, Cl, Si, Br, F, Mg, Fe, and I. All of these elements can therefore be used in a custom alphabet while the check for chemically plausible decompositions still works.

Show Actual Mass and Deviation from Query Mass

If the option Show actual mass for each decomposition. is selected, Decomp will include, for every decomposition, its actual mass. The actual mass may be different from the query mass when the allowed mass error is set to a value greater than zero.

The actual deviation will be shown when Show deviation from query mass for each decomposition is selected.

Introduction
Decompose Reals
Decompose Integers
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References
Manual
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Fri Dec 14 12:50:19 2012