Acyl Fragment Ladder

Count consecutive MS/MS acyl-chain fragment mass differences.

Description

An acyl-fragment ladder screen compares adjacent m/z spacings with a supplied expected step.

An acyl-fragment ladder screen compares adjacent m/z spacings with a supplied expected step. Run length counts peaks, rather than matching gaps.^[1]

Count consecutive MS/MS acyl-chain fragment mass differences.

When to use Acyl Fragment Ladder

Use this tool to count consecutive MS/MS acyl-chain fragment mass differences.

Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.

How to use Acyl Fragment Ladder and understand its results

Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.
Enter fragmentMz, expectedLadderStepMz, stepToleranceMz using the field table and calculation rules, then run the tool.
Read matchedSteps, ladderStartMz, longestRun. 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
fragmentMz	Fragment mz	list of number	Required
expectedLadderStepMz	Expected ladder step mz	number	Required
stepToleranceMz	Step tolerance mz	number	Required

Enter at least two strictly increasing finite fragment values, positive expected step and nonnegative tolerance. Count matching gaps and longest consecutive run, resetting run length to one after a mismatch. Return ladderStartMz as the first input value.

match_i=|mz_i−mz_(i−1)−expectedStep|≤tolerance

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

Output field	Meaning	Value type
matchedSteps	Matched steps	number
ladderStartMz	Ladder start mz	number
longestRun	Longest run	number

json

{
  "input": {
    "fragmentMz": [
      100,
      114,
      128,
      150
    ],
    "expectedLadderStepMz": 14,
    "stepToleranceMz": 0.1
  },
  "output": {
    "matchedSteps": 2,
    "ladderStartMz": 100,
    "longestRun": 3
  }
}

Limitations and assumptions

Positivity of m/z is not enforced. The returned start is not the start of the longest run, and no fragment identities or charge corrections are inferred.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Neutral Loss Matcher: Match product-ion neutral losses against caller-provided diagnostic differences. For a complementary task, use Lipid Unsaturation: Tally lipid-chain carbons and unsaturation sites.

References

Acyl Fragment Ladder — tool.io

Similar or alternative tools

Neutral Loss Matcher
Match product-ion neutral losses against caller-provided diagnostic differences.
Lipid Unsaturation
Tally lipid-chain carbons and unsaturation sites.