Y Ion Series

Build theoretical C-terminal peptide y-ion masses.

Description

Peptide y ions describe theoretical C-terminal fragments.

Peptide y ions describe theoretical C-terminal fragments. For singly protonated unmodified fragments, their residue sum includes terminal water and one proton.^[1]

Build theoretical C-terminal peptide y-ion masses.

When to use Y Ion Series

Use this tool to build theoretical C-terminal peptide y-ion masses.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Y Ion Series and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence, protonMassDa, waterMassDa using the field table and calculation rules, then run the tool.
Read yIonMassesDa. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required
protonMassDa	Proton mass da	number	Required
waterMassDa	Water mass da	number	Required

Enter at least two canonical residues and positive water/proton masses in daltons. Starting at the C terminus, accumulate residue masses and return y1 through y(length−1) in that order.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

y_k=Σ(last k monoisotopic residue masses)+waterMass+protonMass, k=1…length−1

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
yIonMassesDa	Y ion masses da	list of number

json

{
  "input": {
    "sequence": "AGG",
    "protonMassDa": 1,
    "waterMassDa": 18
  },
  "output": {
    "yIonMassesDa": [
      76.02145999999999,
      133.04291999999998
    ]
  }
}

Limitations and assumptions

The series omits the full peptide and assumes one proton. Modifications, isotope envelopes, neutral losses and multiply charged fragments are not modeled.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use B Ion Series: Build theoretical N-terminal peptide b-ion masses. For a complementary task, use Peptide Neutral Mass: Calculate monoisotopic neutral peptide mass from its canonical sequence.

References

Y Ion Series — tool.io

Similar or alternative tools

B Ion Series
Build theoretical N-terminal peptide b-ion masses.
Peptide Neutral Mass
Calculate monoisotopic neutral peptide mass from its canonical sequence.