PNNL.DIA.utils

The goal of PNNL.DIA.utils is

1. A set of functions to analyze DIA-NN and Spectronaut outputs and convert them to MSnSet objects for downstream analysis with MSnSet.utils.
2. Assembling paths for analyzing files directly from DMS.
3. (in-progress) General workflow for plexDIA analysis.

Overview of pnnl.diann.utils package workflow. Package functions are in monospace.

Installation

You can install the development version of PNNL.DIA.utils from GitHub with:

# install.packages("devtools")
devtools::install_github("PNNL-Comp-Mass-Spec/PNNL.DIA.utils")

Example datasets

Example gene group (gg) and protein group (pg) matrices, and precursors (pq) report are found in buildinst/extdata/.

• diann_report.tsv is example data from diann_rpackage
• QC_Mam matrices are from \\proto-8\Lumos02\2023_4\QC_Mam_19_01_b_DIA_trap_60min_19Dec23_Pippin_WBEH-23-05-18\DNN202312200344_Auto2255735

Converting Protein Groups Matrix to MSnSet

library(PNNL.DIA.utils)


pg_matrix_path <- system.file("extdata",
                              "QC_Mam_19_01_b_DIA_report.pg_matrix.tsv",
                              package = "PNNL.DIA.utils")
x <- readr::read_tsv(pg_matrix_path)

PNNL.DIA.utils::pgmatrix_to_msnset(x)

Converting to .htrms on the fly

Spectronaut suggest converting LC-MS files to it’s proprietary .htrms file format to decrease analysis time. Rather then first download local .raw LC-MS files then convert, dms_to_htrms.R fetches the .raw files lsited in a data package from DMS and converts them on-the-fly to local .htrms copies.

Note to run this function you need to have a local version of Spectronaut’s HTRMS Converter.

The example below is how to run this on KAIJU.

# Path to the HTRMSConverter.exe
# This is the local path on KAIJU
# converter_path <- "C:/Program Files (x86)/Biognosys/HTRMS Converter/HTRMSConverter.exe"
 
# Convert a data package
results <- convert_data_package_to_htrms(
   data_package_num = 6447, 
   output_folder = "E:/Data/Converted_Files",
   converter_path = converter_path,
   delay_seconds = 5
)