filter_neutral_loss: Filter Features based on occurrence of neutral losses

In metamorphr: Tidy and Streamlined Metabolomics Data Workflows

Filter Features based on occurrence of neutral losses

Description

The occurrence of characteristic neutral losses can help with the putative annotation of molecules. See the Reference section for an example.

Usage

filter_neutral_loss(
  data,
  losses,
  min_found,
  tolerance = 10,
  tolerance_type = "ppm",
  show_progress = TRUE
)

Arguments

data	A data frame containing MSn spectra.
losses	A numeric. Exact mass of the fragment(s) to filter by.
min_found	How many of the fragments must be found in order to keep the row? If min_found = length(fragments), all fragments must be found.
tolerance	A numeric. The tolerance to apply to the fragments. Either an absolute value in Da (if tolerance_type = "absolute") or in ppm (if tolerance_type = "ppm").
tolerance_type	Either "absolute" or "ppm". Should the tolerance be an absolute value or in ppm?
show_progress	A logical indicating whether the progress of the filtering should be printed to the console. Only important for large tibbles.

Value

A filtered tibble.

References

• A. Brink, F. Fontaine, M. Marschmann, B. Steinhuber, E. N. Cece, I. Zamora, A. Pähler, Rapid Commun. Mass Spectrom. 2014, 28, 2695–2703, DOI 10.1002/rcm.7062.

Examples

# neutral losses must be calculated first
toy_mgf_nl <- toy_mgf %>%
  calc_neutral_loss(m_z_col = PEPMASS)

# all of the given losses (3) must be found
# returns the first row of toy_mgf
toy_mgf_nl %>%
  filter_neutral_loss(losses = c(11.1111, 22.2222, 33.3333), min_found = 3)

# all of the given fragments (3) must be found
# returns an empty tibble because the third loss
# of row 1 (33.3333)
# is outside of the tolerance (10 ppm):
# Lower bound:
# 33.4333 - 33.4333 * 5 / 1000000 = 33.4333
# Upper bound:
# 33.4333 + 33.4333 * 5 / 1000000 = 33.4336
toy_mgf_nl %>%
  filter_neutral_loss(losses = c(11.1111, 22.2222, 33.4333), min_found = 3)

# only 2 of the 3 fragments must be found
# returns the first row of toy_mgf
toy_mgf_nl %>%
  filter_neutral_loss(losses = c(11.1111, 22.2222, 33.4333), min_found = 2)

metamorphr documentation built on June 10, 2026, 5:07 p.m.