Spectral similarity scoring ei simple

Spectral Similarity Scoring (EI Simple)

Summary

The Similarity (EI Simple) algorithm computes pairwise similarity scores between a query electron ionization mass spectrum and library entries to identify and rank matching compounds. It is a core method for unbiased library searching in mass spectrometry when the query spectrum is not an exact match to any library entry.

When to use

Apply this skill when you have a query electron ionization (EI) mass spectrum and need to search it against a library of known EI mass spectra to identify unknown compounds. Use it when exact identity matching (e.g., via the Identity/EI Normal algorithm) fails or when you want ranked similarity scores across all library entries rather than only perfect matches.

When NOT to use

• When you need to identify a spectrum that matches a known library entry exactly — use the Identity (EI Normal) algorithm instead.
• When your input spectra are not electron ionization (EI) spectra (e.g., ESI, APCI, or other ionization modes).
• When the query spectrum is already preprocessed into a pre-computed feature or similarity vector — this skill operates on raw m/z and intensity data.

Inputs

• Query electron ionization mass spectrum (m/z and intensity pairs)
• MSP library file (mass spectrum database in msp format)

Outputs

• Ranked list of library matches with similarity scores
• Pairwise similarity score matrix (query vs. library entries)

How to apply

Load the query EI mass spectrum and an msp library file using mssearchr's msp file reading functionality. Parse both spectra to extract m/z and intensity pairs. Implement or invoke the Similarity (EI Simple) algorithm to compute pairwise similarity scores between the query spectrum and each library entry. The algorithm compares spectral peaks (m/z and intensity) according to the EI Simple scoring scheme; higher scores indicate greater spectral resemblance. Return a ranked list or table of library matches ordered by similarity score (descending). Evaluate the quality of matches by examining the top-ranked candidates and their similarity scores to determine confidence in the assignment.

Related tools

• mssearchr (Provides custom implementation of the Similarity (EI Simple) algorithm and msp file parsing for library search workflows in R) — https://github.com/AndreySamokhin/mssearchr
• R (Computational environment for executing mssearchr workflows and manipulating similarity score results)
• NIST API (Alternative library search backend for electron ionization mass spectra accessible via mssearchr)

Evaluation signals

• Similarity scores are returned for all library entries (no missing values for valid spectra pairs).
• Scores are numeric and bounded in the expected range for the EI Simple metric (typically 0–1 or 0–999 depending on implementation); inspect raw output to confirm normalization.
• Top-ranked library matches align with expected compound identification based on experimental context (e.g., retention time, sample history, known constituents).
• The ranked list is ordered in descending order of similarity score with no ties or inversions that violate the ordering.
• Query spectrum and at least one library entry produce non-zero similarity scores (confirming algorithm executed and scored matches).

Limitations

• The Similarity (EI Simple) algorithm is specific to electron ionization mass spectra; it is not applicable to spectra from other ionization modes.
• Similarity scores depend on the quality and completeness of the library database; missing or poorly annotated library entries can reduce match reliability.
• The algorithm does not account for retention time, isotope patterns, or other orthogonal information; it scores only on m/z and intensity.
• No changelog is available for the mssearchr package, limiting visibility into algorithm refinements or bug fixes across versions.

Evidence

• [intro] custom implementation of the Similarity (EI Simple) algorithm: "The mssearchr package offers the following tools: - custom implementation of the Similarity (EI Simple) algorithm"
• [intro] library searches against electron ionization mass spectral databases: "The primary goal of the mssearchr package is to enhance the capabilities of R users for conducting library searches against electron ionization mass spectral databases."
• [other] Parse both spectra to extract m/z and intensity pairs; Implement the Similarity (EI Simple) algorithm to compute pairwise similarity scores: "Parse both spectra to extract m/z and intensity pairs. 3. Implement the Similarity (EI Simple) algorithm to compute pairwise similarity scores between the query spectrum and each library entry."
• [other] Return a ranked list or table of library matches with their corresponding similarity scores: "Return a ranked list or table of library matches with their corresponding similarity scores."
• [readme] reading/writing msp files: "- reading/writing msp files."