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PepFragCalc Peptide Fragments

Multi-line peptides · a/b/c x/y/z fragment tables · global modification rules

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Peptide sequences (one per line)

One peptide chain per line, each gets its own tables. Single-letter sequences (PEPTIDEKRAQ); inline modifications: S(Phos), C(Carbamidomethyl), [Cit+71.984]; add -NH2 at the end for a C-terminal amide. Blank lines are ignored.

Options

Written once, applied to every matching residue on every line: C+57.0215 (mass shift) or C(Carbamidomethyl) (named modification), comma-separated. Residues that already carry an inline (…) / […] annotation are skipped. Applies to single-letter sequences.
Ion series
Charges
Digest
Modifications: P(Phos), C(Carbamidomethyl), [Cit+71.984]

Results

Enter peptide sequences to get the intact mass and fragment ion table of every line

Available modification names (inline and global rules)

Notation: the residue letter followed by the name in parentheses, e.g. S(Phos); the same names work in global rules, e.g. K(SILAC_K8). For a plain mass shift use [Cit+71.984] inline or a C+57.0215 rule.

Amino acid residue masses

Residue mass = free amino acid − H2O (as inside a peptide bond); intact neutral mass = N-term H + Σ residues + C-term OH. Same NIST dataset as MassCalc.

What this tool is

PepFragCalc computes theoretical peptide fragment ion m/z: enter one or many peptide chains (one per line) and get, for the six proteomics-standard series a/b/c (N-terminal) and x/y/z (C-terminal), the neutral mass plus monoisotopic and average m/z of every position, optionally at 1+/2+/3+ charge states and with -NH3/-H2O secondary ions. It covers everything the UW Proteomics Toolkit "Peptide Fragment" page (FragIonServlet) computes, and adds what it lacks in batch terms: global modification rules applied to every matching residue of every line, and multi-line input with independent tables per peptide.

Everything is computed in your own browser: residue masses, modifications and enzyme tables ship with the page - there is no backend and nothing is uploaded. Input and options are kept in local storage. The intact, fragment and digest numbers come from the same NIST dataset and calculation core as MassCalc (our formula toolkit on this site); the three complementary pairs are strictly self-consistent: b+y, c+z and a+x neutral masses each add up to the intact peptide.

Features

How to use it

  1. Paste your peptides into the box, one chain per line; annotate modifications inline (S(Phos)) or set a global rule for all lines (C+57.0215).
  2. Choose termini, ion series and charge states; tick secondary ions if you want -NH3/-H2O losses; pick an enzyme and missed-cleavage count for digest products.
  3. Every line renders on its own: intact-mass cards, an m/z-sorted fragment ion table (with Δm/z) and the digest table; a bad line only affects itself.
  4. Hit "Copy all results (TSV)" to take every table away - it pastes straight into Excel or your spectrum-processing software.

FAQ

How are the a/b/c and x/y/z series defined?
After peptide-bond cleavage, fragments keeping the N-terminus are named a/b/c by the atoms they lose (b = the intact N-terminal piece, a = b − CO, c = b + NH3); fragments keeping the C-terminus are x/y/z (y = the intact C-terminal piece + H2O, x = y + CO, z = y − NH3). CID/HCD spectra are dominated by the b and y series. The "Side" column of the table tells you which half each ion belongs to.
How do global rules interact with inline modifications?
A rule like C+57.0215 (mass shift) or C(Carbamidomethyl) (named modification) applies to every matching residue of every line; a residue that already carries an inline (…) or […] annotation is skipped, so nothing is added twice. For "most cysteines carbamidomethylated but one free" you can annotate that site inline as [C+0]… the simpler route is to leave global rules empty and annotate site by site.
Monoisotopic or average mass - which one do I use?
High-resolution instruments (Orbitrap, TOF, FT-ICR) match monoisotopic m/z; on low-resolution instruments (ion traps, quadrupoles) heavier peptides appear closer to the average mass. Both columns are printed side by side, so no switching is needed. Above roughly 3 kDa the monoisotopic peak may no longer be the tallest - keep that in mind when searching.
What is the Δm/z column for?
Fragments are sorted by m/z and Δm/z is the difference to the previous row. Consecutive positions of a b/y series differ by exactly one residue mass, so anomalous gaps (+79.97 for a phospho HPO3, −17.03 for an NH3 loss) immediately hint at modifications or secondary ions - a classic manual-interpretation aid.
Are sequences uploaded? How large can peptides be?
No - the page is fully static with no backend; everything is computed locally and the input only goes to browser local storage. Normal peptides (≤ 100 residues) render full tables in milliseconds; top-down whole-protein sequences also work, but the row count grows with length × series × charges, so tick only the series you need.

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