Looking up an unexplained mass difference • commonMZ

You have two peaks in a spectrum and a delta between them, and the question is “what does this gap correspond to?”.

It could be a fragment, usually a neutral loss, (water, CO₂, a whole side chain).
It could also be an adduct (Na⁺ for K⁺, formate for acetate).
Fragments sometimes appear in series of repeating units; e.g. sequential loss of CH₂ in an alkane chain.

All three are catalogued in commonMZ and accessible as individual datasets:

adducts_fragments — adduct and neutral-loss mass differences, mode-agnostic
repeating_units_pos — homologous-series steps in positive mode
repeating_units_neg — homologous-series steps in negative mode

mz_diff_table() merges them into one searchable reference, optionally filtered by mode:

commonMZ::adducts_fragments     # adducts and neutral losses only

# A tibble: 88 × 3
   mz_diff origin                                                      reference
     <dbl> <chr>                                                       <chr>
 1   0.984 "OH <-> NH2, e.g. de-amidiation, CHNO compounds"            F
 2   1.98  "K+ <-> Cl-+2H2+, salt adduct"                              AA
 3   2.00  "F <-> OH, halogen exchange with hydroxy group (typically … F
 4   2.02  "\xb1 2H, opening or forming of double bond"                F
 5   4.96  "Na+<-> NH4+, salt adduct"                                  F
 6   7.00  "F <-> CN, halogen exchange with cyano group"               F
 7   8.97  "Cl <-> CN, halogen exchange with cyano group"              F
 8  14.0   "O <-> 2H, e.g. Oxidation follwed by H2O elimination"       F
 9  14.0   "Cl-+2H2+ <-> Na+, salt adduct"                             AA
10  14.0   "\xb1 CH2, alkane chains, waxes, fatty acids, methylation"  F
# ℹ 78 more rows

commonMZ::repeating_units_pos   # repeating units, positive mode only

# A tibble: 28 × 3
   mz_diff origin                                                      reference
     <dbl> <chr>                                                       <chr>
 1    14.0 -[CH2]-, alkane chains, waxes, fatty acids, methylation     F
 2    16.0 O, oxidation                                                F
 3    18.0 H2O, water clusters                                         F
 4    28.0 -[C2H4]-, natural alkane chains such as fatty acids         F
 5    32.0 CH3OH, methanol clusters                                    F
 6    41.0 CH3CN, acetonitrile clusters                                F
 7    42.0 -[C3H6]-, propyl repeating units, propylation               F
 8    44.0 -[C2H4O]-; polyethylene glycol, PEG, and related component… D, F
 9    50.0 -[CF2]-, from perfluoro compounds                           F
10    53.0 NH4Cl salt adducts/clusters                                 F
# ℹ 18 more rows

diffs <- mz_diff_table("both")  # all three merged; use "pos" or "neg" to filter

The calculator: search by a difference and a ppm tolerance

This is mz_diff_lookup()’s job for a single value called from R.

An instrument’s mass accuracy is quoted as ppm of a measured m/z, so the ppm error of a mass difference only means something when you say which m/z it is relative to. That is what ref_mz is for: pass the m/z of the parent ion the two peaks were measured at, and both the ppm tolerance and the returned error_ppm column are expressed relative to it. In the examples below ref_mz = 300 stands in for a typical parent ion, so error_ppm reads as “how far off would this assignment be for a compound around m/z 300”. Without ref_mz the ppm is taken of the difference itself, which inflates it badly for small deltas — a 0.002 Da error on a 1 Da difference is 2000 ppm of the delta but only 6.7 ppm at m/z 300. See ?mz_diff_lookup for the full argument.

mz_diff_lookup(18.0106, tol = 100, ref_mz = 300) %>%   # water, 100 ppm at m/z 300
  mutate(error_Da = signif(error_Da, 2), error_ppm = round(error_ppm, 1))

The 100 ppm window is 0.03 Da at m/z 300, wide enough to also catch the F ↔︎ H halogen exchange two hundredths of a Da away — at −67 ppm, clearly distinguishable from water’s −0.1 ppm.

And a genuinely ambiguous case: a 44 Da delta returns three completely different explanations — CO₂ neutral loss (decarboxylation), a double-sodium salt adduct, and a PEG repeat-unit step (polymer contamination from the LC system). A flat Da window is used here because the three entries span 62 mDa, more than even a 50 ppm window at m/z 300 (15 mDa) would cover; ref_mz = 300 is still passed so the reported error_ppm stays on the same realistic scale. The key point is that mass alone cannot decide between them:

mz_diff_lookup(44, tol = 0.05, unit = "Da", ref_mz = 300) %>%
  mutate(error_Da = signif(error_Da, 2), error_ppm = round(error_ppm, 1))

Working interactively

Here is a little interactive table to search for these differences:

m/z difference (Da)

tolerance (ppm)

reference m/z (Da)

The search only re-filters when you click Search (not on every keystroke), so typing a value never triggers a redraw mid-edit; click once you’ve entered both numbers, or press Clear to go back to the full table.

Glossary

Ion types

Notation	Meaning
`f+`	fragment ion
`[f+H]+`	protonated fragment ion (e.g. in-source fragmentation)
`[M+H]+`	protonated molecular ion (pseudomolecular ion)
`[M+Na]+`	sodiated molecular ion
`[M+K]+`	potassiated molecular ion
`[2M+H]+`, `[3M+H]+`	protonated dimer, trimer, etc.
`[AnBm+H]+`	protonated ion of a complex with n A and m B subunits

Abbreviations used in the origin column

Abbreviation	Meaning
4-HCCA	α-cyano-4-hydroxycinnamic acid — common MALDI matrix
2,5-DHB	2,5-dihydroxybenzoic acid — common MALDI matrix
MeCN, ACN	acetonitrile (solvent)
MeOH	methanol (solvent)
MeNO₂	nitromethane (solvent)
HABA	2-(4-hydroxyphenylazo)benzoic acid — MALDI matrix
SA	sinapic / sinapinic acid — common MALDI matrix
PEG	polyethylene glycol; repeat unit –[O–CH₂–CH₂]–, 44 Da
PPG	polypropylene glycol; repeat unit –[O–C(CH₃)H–CH₂]–, 58 Da
XaaCcamXaa	carbamidomethylated cysteine residue (+57 Da)
XaaMoxXaa	singly oxidised methionine residue (+16 Da)

References for the reference column

Ref	Author(s)	Citation or website
A	Waters Corporation	Background Ion List
B	Applied Biosystems	Appendix D: Commonly Observed Background Ions — Mariner Biospectrometry Workstation Users Guide
C	New Objective	Common Background Ions for Electrospray (Technical Note)
D	Sigma-Aldrich	Chemical formulas for Tween, Triton, and reduced Triton from the Sigma-Aldrich catalogue
E	Thermo Corporation; Mahn, B.	List of LC/MS contaminants
F	Tong, H.; Bell, D.; Tabei, K.; Siegel, M. M.	J. Am. Soc. Mass Spectrom., 10 (1999) 1174
G	Andersen, J. S.; Kuester, B.; Podtelejnikov, A.; Mortz, E.; Mann, M.	Proc. 47th ASMS Conf. Mass Spectrom. Allied Topics, 1999, Dallas, TX
H	Keller, B. O.; Li, L.	J. Am. Soc. Mass Spectrom., 11 (2000) 88
I	Keller, B. O.; Li, L.; Keller, H.	MaClust: matrix cluster mass prediction
J	Harris, W. A.; Janecki, D. J.; Reilly, J. P.	Rapid Commun. Mass Spectrom., 16 (2002) 1714
K	Keller, B. O.; Sui, J.; Young, A. B.; Whittal, R. M.	Unpublished results; ESI background ions — Tween, Triton, PEGs, PPGs
L	Schlosser, A.; Volkmer-Engert, R.	J. Mass Spectrom., 38 (2003) 523
M	Tran, J. C.; Doucette, A. A.	J. Am. Soc. Mass Spectrom., 17 (2006) 652
N	Verge, K. M.; Agnes, G. R.	J. Am. Soc. Mass Spectrom., 13 (2002) 901
O	Paez, A.; Howe, A.	Canadian Chemical News, 56 (2004) 14
P	Purves, R. W.; Gabryelski, W.; Li, L.	Rev. Sci. Instrum., 68 (1997) 3252
Q	Gibson, C. R.; Brown, C. M.	J. Am. Soc. Mass Spectrom., 14 (2003) 1247
R	Beavis, R. C.; Chait, B. T.	Anal. Chem., 62 (1990) 1836
S	Guzzetta, A.	ionsource.com — Carbohydrate marker ions
T	Clauser, K. R.; Hall, S. C.; Smith, D. M.; Webb, J. W.; Andrews, L. E.; Tran, H. M.; Epstein, L. B.; Burlingame, A. L.	Proc. Natl. Acad. Sci. USA, 92 (1995) 5072
U	Macha, S. F.; Limbach, P. A.; Hanton, S. D.; Owens, K. G.	J. Am. Soc. Mass Spectrom., 12 (2001) 732
V	Pleasance, S.; Thibault, P.; Sim, P. G.; Boyd, R. K.	Rapid Commun. Mass Spectrom., 5 (1991) 307
W	Xia, Y.; Patel, S.; Bakhtiar, R.; Franklin, R. B.; Doss, G. A.	J. Am. Soc. Mass Spectrom., 16 (2005) 417
X	Guo, X.; Bruins, A. P.; Covey, T. R.	Rapid Commun. Mass Spectrom., 20 (2006) 3145
Y	Ijames, C. F.; Dutky, R. C.; Fales, H. M.	J. Am. Soc. Mass Spectrom., 6 (1995) 1226
Z	Hesse, M.; Meier, H.; Zeeh, B.	Spektroskopische Methoden in der organischen Chemie, Georg Thieme Verlag, Stuttgart, 3rd ed. 1987, ISBN: 3-13-576103-7
AA	Stanstrup, J.	commonMZ R package