HolobiomicsLab 
Base-Peak Intensity Identification
Summary
Extract the base-peak m/z and intensity values (maximum intensity peak) from individual MS1 scans in Thermo Fisher raw files and organize them into a tabular data frame. This skill enables direct access to fundamental spectral descriptors without conversion to exchange formats.
When to use
When you have Thermo Fisher Scientific .raw files from an Orbitrap instrument and need to identify the m/z value and corresponding intensity of the most abundant ion in each MS1 scan for quality control, method optimization, or feature extraction in a modular R-based proteomics pipeline.
When NOT to use
- Input is already in mzML, mzXML, or other exchange format—use format-agnostic parsers (e.g., MSnbase) instead of rawrr, which is specific to Thermo .raw files.
- You need to extract all peaks or construct full MS1 feature tables—base-peak extraction is a single-value summary per scan; use readSpectrum() with full spectral processing for comprehensive feature matrices.
- Working with non-Thermo instruments (e.g., Bruker, Waters, ABSciex)—rawrr wraps the Thermo RawFileReader API and cannot read other vendor formats.
Inputs
- Thermo Fisher Scientific .raw file (proprietary binary format)
- MS scan index (data.frame with scan metadata including ms_level)
- MS1 scan identifiers (positive integers)
Outputs
- data.frame with columns: scan index, base-peak m/z, base-peak intensity
- rawrrSpectrum objects (intermediate)
- numeric vectors of m/z and intensity pairs
How to apply
Install the rawrr R package and its compiled executable via rawrr::installRawrrExe(). Load the .raw file and generate a scan index using readIndex() to retrieve all scans. Filter the index to retain only MS1-level scans by subsetting on ms_level==1. Iterate through each filtered scan number and call readSpectrum() to extract spectral data as a rawrrSpectrum object. For each spectrum, use accessor functions ($ or [[) to retrieve the m/z and intensity arrays, identify the m/z position corresponding to the maximum intensity value, and extract both the base-peak m/z and its intensity. Aggregate the scan index, base-peak m/z, and base-peak intensity into a data frame for downstream analysis or visualization.
Related tools
- rawrr (Primary R package providing accessor functions and subsetting operators to extract spectral attributes from rawrrSpectrum objects and convert scan data into tabular formats) — https://github.com/fgcz/rawrr
- RawFileReader (.NET assembly wrapped by rawrr; provides low-level API to read binary Thermo .raw file data via system calls) — https://github.com/thermofisherlsms/RawFileReader
- MsBackendRawFileReader (Optional: serves as an MsBackend for the Bioconductor Spectra package, enabling integration of rawrr-based spectral extraction into modular analysis workflows) — https://github.com/cpanse/MsBackendRawFileReader
Examples
library(rawrr); rawrr::installRawrrExe(); idx <- readIndex('20181113_010_autoQC01.raw'); ms1_idx <- subset(idx, ms_level == 1); basepeak_df <- data.frame(scan = ms1_idx$scan, bp_mz = NA_real_, bp_intensity = NA_real_); for(i in seq_along(ms1_idx$scan)) { spec <- readSpectrum('20181113_010_autoQC01.raw', scans = ms1_idx$scan[i]); max_idx <- which.max(spec$intensity[[1]]); basepeak_df$bp_mz[i] <- spec$mz[[1]][max_idx]; basepeak_df$bp_intensity[i] <- spec$intensity[[1]][max_idx]; }
Evaluation signals
- Extracted data frame has no missing values in base-peak m/z or intensity columns for any MS1 scan.
- Base-peak intensity value for each scan matches the maximum value in the corresponding spectrum's intensity array.
- Base-peak m/z value is the m/z coordinate at the position of maximum intensity in the spectrum.
- Number of rows in output data frame equals the number of MS1 scans in the input .raw file (validate via length of filtered readIndex() result).
- Retention time or scan-level metadata from the index aligns with the extracted base-peak rows (1:1 correspondence by scan number).
Limitations
- rawrr is specific to Thermo Fisher Scientific Orbitrap instruments and cannot read .raw files from other vendors (Bruker, Waters, ABSciex).
- Requires installation of the rawrr compiled executable; platform-specific compilation may be needed on non-standard systems.
- Base-peak extraction is a summary statistic and loses information about the full peak distribution; not suitable for isotope pattern analysis or charge-state deconvolution.
- Performance scales linearly with the number of scans; very large .raw files (>100,000 scans) may require iterative processing or memory management.
- Accessor functions ($, [[]]) assume rawrrSpectrum object structure; malformed or corrupt scans may raise parsing errors or return NA values.
Evidence
- [other] Filter MS scans using ms filter: "Filter the index to retain only MS1-level scans by subsetting on ms_level==1"
- [other] Iterate and extract base-peak values: "Iterate through filtered scans and call readSpectrum() on each scan number to extract spectral data. For each spectrum, extract the base-peak m/z (maximum intensity m/z value) and its corresponding"
- [other] Accessor functions enable tabular extraction: "rawrr provides accessor functions and subsetting operators ($, [[) to programmatically extract spectral attributes from rawrrSpectrum objects, enabling conversion of scan data into tabular formats."
- [other] Installation procedure: "Install the rawrr executable using rawrr::installRawrrExe()"
- [readme] Direct binary file access rationale: "provides direct access to spectral data stored in Thermo Fisher Scientific raw-formatted binary files, thereby eliminating the need for unfavorable conversion to exchange formats"
- [readme] Spectral data representation: "spectral data is presented by using only two non-standard objects representing data items well known to analytical scientists (mass spectrum and mass chromatogram)"