raw-data-throughput-benchmarking
Summary
Measure the spectra-per-second throughput of raw mass spectrometry data reading operations using controlled benchmark experiments with varying scan counts. This skill quantifies I/O and parsing performance on proprietary binary formats (e.g., Thermo .raw files) to validate data access layer speed and guide pipeline optimization decisions.
When to use
When you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.g., rawrr::readSpectrum) in spectra per second to verify performance meets expected baselines, compare implementations, or predict processing time for large datasets.
When NOT to use
- Input is already a processed feature table or peak list; benchmarking is for raw binary file access, not downstream statistical analysis.
- The raw file format is not supported by the installed library (e.g., attempting to benchmark rawrr on non-Thermo formats without appropriate backend).
- Performance is not a primary concern; benchmarking is overhead-heavy and unnecessary if only correctness of a single read operation is needed.
Inputs
- Thermo .raw file (binary proprietary format containing FTMS spectra)
- Installed raw data access library (e.g., rawrr R package)
- Required runtime (e.g., .NET 8.0 for rawrr)
- Target reading function name (e.g., 'readSpectrum')
Outputs
- Throughput metric in spectra per second
- Benchmark runtime summary (total seconds, per-run times)
- Performance comparison table or report
How to apply
Install and verify the data access library and its runtime dependencies (e.g., rawrr package, .NET 8.0 runtime via rawrr::installRawrrExe()). Load a representative raw file (e.g., the provided QC standard 20181113_010_autoQC01.raw, containing Fourier-transformed Orbitrap FTMS data). Execute the library's built-in benchmark function (e.g., rawrr:::.benchmark) targeting the reading function of interest, passing multiple runs with varying randomly generated scan ID counts. Capture the returned spectra-per-second metric from each run. Record the overall runtime and compute summary statistics (mean, variance) across runs. Compare measured throughput against reference values in the literature or prior implementations to assess consistency and identify performance regressions.
Related tools
- rawrr (R package that wraps RawFileReader .NET assembly and provides the benchmark infrastructure (rawrr:::.benchmark function) and readSpectrum() target function) — https://github.com/fgcz/rawrr
- RawFileReader (Thermo Fisher Scientific .NET assembly that performs low-level binary file I/O and spectral data extraction, invoked via C# wrapper methods by rawrr) — https://github.com/thermofisherlsms/RawFileReader
- .NET 8.0 Runtime (Required runtime environment for executing compiled C# wrapper methods that interface with RawFileReader assembly)
Examples
rawrr::installRawrrExe(); S <- rawrr::readSpectrum(rawfile = '20181113_010_autoQC01.raw', scan = 1:100); bench <- rawrr:::.benchmark(fun = rawrr::readSpectrum, rawfile = '20181113_010_autoQC01.raw'); print(bench)
Evaluation signals
- Benchmark completes without errors and returns a numeric throughput value (spectra/second) for each run.
- Measured throughput is consistent across multiple runs with the same scan count (low variance), indicating stable I/O and parsing performance.
- Measured throughput aligns with or exceeds published reference values from the rawrr paper (task_002 finding) or prior benchmark reports, confirming no performance regression.
- Throughput scales predictably with scan count (higher scans → higher absolute spectra/second or stable rate), ruling out systematic bottlenecks.
- Total benchmark runtime and per-run timings are reasonable (sub-second to seconds) and do not indicate excessive resource contention or GC pauses.
Limitations
- Benchmark results are hardware-dependent (CPU, disk I/O speed, RAM); throughput cannot be directly compared across different systems without normalization.
- Windows systems require decimal symbol configuration as '.' for proper data extraction, which may affect reproducibility if misconfigured.
- The benchmark is tied to a specific library version and runtime (.NET 8.0); upgrading either may alter throughput metrics, complicating longitudinal comparisons.
- Benchmark uses randomly generated scan IDs; real-world access patterns (sequential vs. random, clustered vs. sparse) may exhibit different throughput due to caching and I/O locality effects.
Evidence
- [other] Execute rawrr:::.benchmark function with rawrr::readSpectrum as the target function, which invokes compiled C# wrapper methods via system2 call to interact with the RawFileReader .NET assembly.: "Execute rawrr:::.benchmark function with rawrr::readSpectrum as the target function, which invokes compiled C# wrapper methods via system2 call to interact with the RawFileReader .NET assembly."
- [other] The benchmark experiment using rawrr::readSpectrum demonstrates throughput measured in spectra per second across multiple runs with varying numbers of randomly generated scan IDs, with overall runtime totaling approximately 0.5 seconds.: "The benchmark experiment using rawrr::readSpectrum demonstrates throughput measured in spectra per second across multiple runs with varying numbers of randomly generated scan IDs, with overall"
- [other] Load the example raw file 20181113_010_autoQC01.raw (Fourier-transformed Orbitrap FTMS data from a Q Exactive HF instrument) using rawrr package initialization.: "Load the example raw file 20181113_010_autoQC01.raw (Fourier-transformed Orbitrap FTMS data from a Q Exactive HF instrument) using rawrr package initialization."
- [other] Install the rawrr executable and verify .NET 8.0 runtime availability via rawrr::installRawrrExe().: "Install the rawrr executable and verify .NET 8.0 runtime availability via rawrr::installRawrrExe()."
- [methods] Specifically,
R functions requesting access to data stored in binary raw files (reader family functions listed in Table 1) invoke compiled C# wrapper methods using a system call: "Specifically, R functions requesting access to data stored in binary raw files (reader family functions listed in Table 1) invoke compiled C# wrapper methods using a system call"
- [discussion] On Windows, the decimal symbol has to be configured as a '.'!: "On Windows, the decimal symbol has to be configured as a '.'!"
1---2name: raw-data-throughput-benchmarking-23description: Use when when you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.4license: CC-BY-4.05---67# raw-data-throughput-benchmarking89## Summary1011Measure the spectra-per-second throughput of raw mass spectrometry data reading operations using controlled benchmark experiments with varying scan counts. This skill quantifies I/O and parsing performance on proprietary binary formats (e.g., Thermo .raw files) to validate data access layer speed and guide pipeline optimization decisions.1213## When to use1415When you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.g., rawrr::readSpectrum) in spectra per second to verify performance meets expected baselines, compare implementations, or predict processing time for large datasets.1617## When NOT to use1819- Input is already a processed feature table or peak list; benchmarking is for raw binary file access, not downstream statistical analysis.20- The raw file format is not supported by the installed library (e.g., attempting to benchmark rawrr on non-Thermo formats without appropriate backend).21- Performance is not a primary concern; benchmarking is overhead-heavy and unnecessary if only correctness of a single read operation is needed.2223## Inputs2425- Thermo .raw file (binary proprietary format containing FTMS spectra)26- Installed raw data access library (e.g., rawrr R package)27- Required runtime (e.g., .NET 8.0 for rawrr)28- Target reading function name (e.g., 'readSpectrum')2930## Outputs3132- Throughput metric in spectra per second33- Benchmark runtime summary (total seconds, per-run times)34- Performance comparison table or report3536## How to apply3738Install and verify the data access library and its runtime dependencies (e.g., rawrr package, .NET 8.0 runtime via rawrr::installRawrrExe()). Load a representative raw file (e.g., the provided QC standard 20181113_010_autoQC01.raw, containing Fourier-transformed Orbitrap FTMS data). Execute the library's built-in benchmark function (e.g., rawrr:::.benchmark) targeting the reading function of interest, passing multiple runs with varying randomly generated scan ID counts. Capture the returned spectra-per-second metric from each run. Record the overall runtime and compute summary statistics (mean, variance) across runs. Compare measured throughput against reference values in the literature or prior implementations to assess consistency and identify performance regressions.3940## Related tools4142- **rawrr** (R package that wraps RawFileReader .NET assembly and provides the benchmark infrastructure (rawrr:::.benchmark function) and readSpectrum() target function) — https://github.com/fgcz/rawrr43- **RawFileReader** (Thermo Fisher Scientific .NET assembly that performs low-level binary file I/O and spectral data extraction, invoked via C# wrapper methods by rawrr) — https://github.com/thermofisherlsms/RawFileReader44- **.NET 8.0 Runtime** (Required runtime environment for executing compiled C# wrapper methods that interface with RawFileReader assembly)4546## Examples4748```49rawrr::installRawrrExe(); S <- rawrr::readSpectrum(rawfile = '20181113_010_autoQC01.raw', scan = 1:100); bench <- rawrr:::.benchmark(fun = rawrr::readSpectrum, rawfile = '20181113_010_autoQC01.raw'); print(bench)50```5152## Evaluation signals5354- Benchmark completes without errors and returns a numeric throughput value (spectra/second) for each run.55- Measured throughput is consistent across multiple runs with the same scan count (low variance), indicating stable I/O and parsing performance.56- Measured throughput aligns with or exceeds published reference values from the rawrr paper (task_002 finding) or prior benchmark reports, confirming no performance regression.57- Throughput scales predictably with scan count (higher scans → higher absolute spectra/second or stable rate), ruling out systematic bottlenecks.58- Total benchmark runtime and per-run timings are reasonable (sub-second to seconds) and do not indicate excessive resource contention or GC pauses.5960## Limitations6162- Benchmark results are hardware-dependent (CPU, disk I/O speed, RAM); throughput cannot be directly compared across different systems without normalization.63- Windows systems require decimal symbol configuration as '.' for proper data extraction, which may affect reproducibility if misconfigured.64- The benchmark is tied to a specific library version and runtime (.NET 8.0); upgrading either may alter throughput metrics, complicating longitudinal comparisons.65- Benchmark uses randomly generated scan IDs; real-world access patterns (sequential vs. random, clustered vs. sparse) may exhibit different throughput due to caching and I/O locality effects.6667## Evidence6869- [other] Execute rawrr:::.benchmark function with rawrr::readSpectrum as the target function, which invokes compiled C# wrapper methods via system2 call to interact with the RawFileReader .NET assembly.: "Execute rawrr:::.benchmark function with rawrr::readSpectrum as the target function, which invokes compiled C# wrapper methods via system2 call to interact with the RawFileReader .NET assembly."70- [other] The benchmark experiment using rawrr::readSpectrum demonstrates throughput measured in spectra per second across multiple runs with varying numbers of randomly generated scan IDs, with overall runtime totaling approximately 0.5 seconds.: "The benchmark experiment using rawrr::readSpectrum demonstrates throughput measured in spectra per second across multiple runs with varying numbers of randomly generated scan IDs, with overall"71- [other] Load the example raw file 20181113_010_autoQC01.raw (Fourier-transformed Orbitrap FTMS data from a Q Exactive HF instrument) using rawrr package initialization.: "Load the example raw file 20181113_010_autoQC01.raw (Fourier-transformed Orbitrap FTMS data from a Q Exactive HF instrument) using rawrr package initialization."72- [other] Install the rawrr executable and verify .NET 8.0 runtime availability via rawrr::installRawrrExe().: "Install the rawrr executable and verify .NET 8.0 runtime availability via rawrr::installRawrrExe()."73- [methods] Specifically, `R` functions requesting access to data stored in binary raw files (reader family functions listed in Table 1) invoke compiled `C#` wrapper methods using a system call: "Specifically, `R` functions requesting access to data stored in binary raw files (reader family functions listed in Table 1) invoke compiled `C#` wrapper methods using a system call"74- [discussion] On Windows, the decimal symbol has to be configured as a '.'!: "On Windows, the decimal symbol has to be configured as a '.'!"
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