2 - Using the MS2extract batch pipeline
Cristian Quiroz-Moreno & Jessica Cooperstone
2024-04-23
Source:vignettes/Busing_batch_extract.Rmd
Busing_batch_extract.RmdIntroduction
In the previous tutorial Introduction to MS2extract package, we described in a detailed manner the core functions of the package. If you are starting to use the MS2extract package with this tutorial, we encourage you to take a look at this tutorial first.
Once you are familiar with the core workflow and functions of this
package, we can dive into an automated pipeline with the proposed
batch_*() functions. If you find that you want to extract
many MS/MS spectra at once, you will want to use
thesebatch_*() functions
The first three main steps have a separate batch_*()
alternative functions; importing mzXML files, extracting MS/MS spectra,
and detecting masses. However, exporting your library to a
.msp or .mgf file is able to detect if the
provided spectra comes from a single or multiple
.mzXML/.mzML files, so the same function works
in both cases.
Figure 1. Overview of general data processing pipeline to extract MS/MS spectra using the MS2extract package
Batch functions
We are familiar with the arguments that the core functions accept, in
this section we describe extra arguments that specific
batch_*() functions require.
batch_import_mzxml
Similarly to import_mzxml(), we need to provide the
compound metadata, with at minimum the compound name, formula,
ionization mode, and collision energy. Optionally, but recommended, the
region of interest where each compound elute (min_rt and
max_rt).
# Select the csv file name and path
batch_file <- system.file("extdata", "batch_read.csv",
package = "MS2extract"
)
# Read the data frame
batch_data <- read.csv(batch_file)
# File paths for Procyanidin A2 and Rutin
ProcA2_file <- system.file("extdata",
"ProcyanidinA2_neg_20eV.mzXML",
package = "MS2extract"
)
Rutin_file <- system.file("extdata",
"Rutin_neg_20eV.mzXML",
package = "MS2extract"
)
# Add file path - User should specified the file path -
batch_data$File <- c(ProcA2_file, Rutin_file)
# Checking batch_data data frame
dplyr::glimpse(batch_data)
#> Rows: 2
#> Columns: 7
#> $ Name <chr> "Procyanidin A2", "Rutin"
#> $ Formula <chr> "C30H24O12", "C27H30O16"
#> $ Ionization_mode <chr> "Negative", "Negative"
#> $ min_rt <int> 163, 162
#> $ max_rt <int> 180, 171
#> $ COLLISIONENERGY <chr> " 20 eV", " 20 eV"
#> $ File <chr> "/home/runner/work/_temp/Library/MS2extract/extdata/Pr…The only difference between batch_import_mzxml() and
import_mzxml() is that met_metadata can be
more than one row. In this example, we are working with two compounds,
procyanidin A2 and rutin.
Tip: you can extract multiple compounds from the same .mzXML if they have different precursor ion m/z.
Tip: you can also specify multiple compounds that have the same m/z as long as they have different retention time.
batch_compounds <- batch_import_mzxml(batch_data)
#>
#> ── Begining batch import ───────────────────────────────────────────────────────
#>
#> ── -- ──
#>
#> • Processing: ProcyanidinA2_neg_20eV.mzXML
#> • Found 1 CE value: 20
#> • Remember to match CE velues in spec_metadata when exporting your library
#> • m/z range given 10 ppm: 575.11376 and 575.12526
#> • Compound name: Procyanidin A2_Negative_20
#>
#> ── -- ──
#>
#> • Processing: Rutin_neg_20eV.mzXML
#> • Found 1 CE value: 20
#> • Remember to match CE velues in spec_metadata when exporting your library
#> • m/z range given 10 ppm: 609.14002 and 609.15221
#> • Compound name: Rutin_Negative_20
#>
#> ── End batch import ────────────────────────────────────────────────────────────The raw mzXML data contains:
- Procyanidin A2: 24249 ions
- Rutin: 22096 ions
# Checking dimension by compound
purrr::map(batch_compounds, dim)
#> $`Procyanidin A2_Negative_20`
#> [1] 24249 6
#>
#> $Rutin_Negative_20
#> [1] 22096 6batch_extract_MS2()
Now that we have our data in imported, we can proceed to extract the
most intense MS/MS scan for each compound. In this case, the
batch_extract_MS2() functions do not have extra arguments,
although most of the arguments remains fairly similar.
# Use extract batch extract_MS2
batch_extracted <- batch_extract_MS2(batch_compounds,
verbose = TRUE,
out_list = FALSE
)
By using verbose = TRUE, we can display the MS/MS TIC
plot as well the raw MS/MS spectra of the most intense scan for each
compound.
batch_detect_mass()
Now that we have the raw MS/MS spectra, we are going to remove
background noise based on intensity. batch_detect_mass()
has the same arguments than its core analogue.
batch_mass_detected <- batch_detect_mass(batch_extracted, # Compound list
normalize = TRUE, # Normalize
min_int = 1 # 1% minimum intensity
)
purrr::map(batch_mass_detected, dim)
#> $`Procyanidin A2_Negative_20`
#> [1] 38 6
#>
#> $Rutin_Negative_20
#> [1] 4 6We see a decrease of number of ions, 38 and 4 ions for procyanidin A2 and rutin, respectively.
write_msp
In contrast with the previous batch functions,
write_msp() is able to detect if the user is providing a
single or multiple spectra. However, the user needs to provide metadata
about each compound to be included in the resulting .msp database.
# Reading batch metadata
metadata_msp_file <- system.file("extdata",
"batch_msp_metadata.csv",
package = "MS2extract"
)
metadata_msp <- read.csv(metadata_msp_file)
dplyr::glimpse(metadata_msp)
#> Rows: 2
#> Columns: 8
#> $ NAME <chr> "Procyanidin A2", "Rutin"
#> $ PRECURSORTYPE <chr> "[M-H]-", "[M-H]-"
#> $ FORMULA <chr> "C30H24O12", "C27H30O16"
#> $ INCHIKEY <chr> "NSEWTSAADLNHNH-LSBOWGMISA-N", "IKGXIBQEEMLURG-NVPNHPE…
#> $ SMILES <chr> "C1C(C(OC2=C1C(=CC3=C2C4C(C(O3)(OC5=CC(=CC(=C45)O)O)C6…
#> $ IONMODE <chr> "Negative", "Negative"
#> $ INSTRUMENTTYPE <chr> "LC-ESI-QTOF", "LC-ESI-QTOF"
#> $ COLLISIONENERGY <chr> "20 eV", "20 eV"After having the cleaned MS/MS spectra and the compound metadata, we can proceed to export them into a .msp file.
write_msp(
spec = batch_mass_detected,
spec_metadata = metadata_msp,
msp_name = "ProcA2_Rutin_batch.msp"
)Session info
sessionInfo()
#> R version 4.3.3 (2024-02-29)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.4 LTS
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