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Mzion

true 2024-10-17

Installation

To install this package, start R and enter:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("qzhang503/mzion")

# or install both Mzion and its ShinyApp:
devtools::install_github("qzhang503/mzionShiny")

Peaklist formats

  • Thermo’s MS

    • RAW (default)

    • MSConvert mzML (critical fixes only)

      [+] Binary encode 64-bit

      [+] Write index

      [+] TPP compatibility

      [-] Use zlib compression (do not compress)

      [+] Filters

      1. peakPicking: vendor msLevel = 1-

      2. (optional) zeroSamples: removeExtra 1-

    • MSConvert mgf (softly depreciated)

  • Bruker’s PASEF-MS
    • .d

Database searches via a ShinyApp

mzionShiny::run_app()

Help documents

Enter ?mzion::matchMS from an RStudio console.

Data QC and mining

Optional database searches via R scripts

## Global, TMT-10plex
library(mzion)

matchMS(
  out_path  = "~/mzion/examples/out", 
  mgf_path  = "~/mzion/examples/raw",
  fasta     = c("~/mzion/dbs/fasta/refseq/refseq_hs_2013_07.fasta", 
                "~/mzion/dbs/fasta/refseq/refseq_mm_2013_07.fasta", 
                "~/mzion/dbs/fasta/crap/crap.fasta"), 
  
  # (see also ?load_fasta2)
  acc_type  = c("refseq_acc", "refseq_acc", "other"), 
  
  # "TMT6plex" at mass 229.162932 Da for TMT-6, -10 and -11 
  # (see also ?table_unimods)
  fixedmods = c("TMT6plex (N-term)", "TMT6plex (K)", "Carbamidomethyl (C)"),
  varmods   = c("Acetyl (Protein N-term)", "Oxidation (M)",
               "Deamidated (N)", "Gln->pyro-Glu (N-term = Q)"),
  max_miss  = 4, 
  quant     = "tmt10", 
  fdr_type  = "protein", 
)


## Phospho, TMT
matchMS(
  out_path  = "~/mzion/examples_p/out", 
  mgf_path  = "~/mzion/examples_p/raw",
  fasta     = c("~/mzion/dbs/fasta/uniprot/uniprot_hsmm_2020_03.fasta", 
                "~/mzion/dbs/fasta/crap/crap.fasta"), 
  acc_type  = c("uniprot_acc", "other"), 
  fixedmods = c("TMT6plex (N-term)", "TMT6plex (K)", "Carbamidomethyl (C)"), 
  varmods   = c("Acetyl (Protein N-term)", "Oxidation (M)", 
                "Deamidated (N)", "Phospho (S)", "Phospho (T)", 
                "Phospho (Y)", "Gln->pyro-Glu (N-term = Q)"), 
  locmods   = c("Phospho (S)", "Phospho (T)", "Phospho (Y)"), 
  max_miss  = 4, 
  quant     = "tmt10", 
  fdr_type  = "protein",
)

## See also ?matchMS for SILAC, acetylome workflows etc.

Specifications of fixed and variable modifications

The Unimod definition of positions and sites were adopted by Mzion for specifying fixed and variable modifications. The value of a position is in one of “Anywhere”, “Protein N-term”, “Protein C-term”, “Any N-term” or “Any C-term”. The last two position labels can be shorthanded as “N-term” and “C-term”. A site is a one-letter representation of the twenty amino-acid residues, as well as the terminal sites of “N-term” and “C-term”. The general format in specifying a fixed or variable modification is title (position = site) where title is a unique character string without space. At a position of “Anywhere”, the modification can be shorthanded as title (site), for example, TMT10plex (K). For a terminal modification at any site, it can be abbreviated as title (position), for examples, Acetyl (Protein N-term) and TMT10plex (N-term). There are circumstances that both position and site are needed for specifying a modification, for instance, Gln->pyro-Glu (N-term = Q). More examples are available in the help document of Mzion utility of parse_unimod.

Other utilities

  • mapMS2ions: visualizes MS2 spectrum matches
  • table_unimods summarizes Unimod entries
  • find_unimod: finds a Unimod entry
  • parse_unimod: parses a Unimod entry
  • calc_unimod_compmass: calculates the composition masses of a Unimod
  • add_unimod: adds a Unimod entry
  • remove_unimod: removes a Unimod entry
  • remove_unimod_title: removes a Unimod entry by title
  • make_mztab: prepares a mzTab file from the search results

Cite Mzion

Zhang, Q. Mzion enables deep and precise identification of peptides in data-dependent acquisition proteomics. Sci. Rep. 13, 7056 (2023).