Mass Spectrometer Search Timing for Real-Time Peptide Identification

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Solution Overview

Problem

In mass spectrometry, real-time database searches for peptide identification are often time-consuming, limiting the throughput of data-dependent acquisition and leading to reduced data points and sample waste due to the brief availability of peptides for analysis.

Innovation Solution

Implementing a method where a mass spectrometer performs real-time searches of a mass spectral database during the introduction period of peptide ions, monitoring elapsed search time, and taking actions based on identification before reaching a maximum search time value, such as adjusting fragmentation techniques or terminating searches, to optimize peptide analysis.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If real-time database searches are performed during the introduction period of peptide ions, then the throughput of mass spectrometry is enhanced and sample waste is reduced, but the search time may be insufficient to complete comprehensive peptide identification

Engineering Contradiction:

Improvethroughput of mass spectrometryVSAvoidsearch time

Core Design Contradiction:

ProductivityVSLoss of time

Solution Approach 1:

The patent performs database searches during the introduction period of peptide ions, which is the time window before full MS scans are completed. By utilizing this otherwise wasted time for preliminary search operations, the system identifies peptide ions early and can make data-dependent acquisition decisions without extending the total analysis time. This preliminary action during idle time resolves the contradiction between enhancing throughput and maintaining sufficient search time.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent dynamically adjusts the search strategy based on the elapsed search time and identification results. The system can terminate searches early when sufficient identifications are made, or continue searching if more time is available within the introduction period. This dynamic adaptation allows the system to optimize the balance between search completeness and throughput, resolving the time contradiction.

Inventive Principle:

Principle #15Dynamics

2Measurement precision

If the mass spectrometer performs comprehensive database searches, then peptide identification accuracy is improved, but the number of scans performed is reduced and data points are lost

Engineering Contradiction:

Improvepeptide identification accuracyVSAvoidnumber of scans performed

Core Design Contradiction:

Measurement precisionVSProductivity

Solution Approach 1:

The patent performs partial database searches during the introduction period rather than waiting to complete full scans. This partial action during the introduction period provides sufficient identification accuracy for data-dependent acquisition decisions while preserving instrument time for additional scans. The system performs just enough searching to make informed decisions without sacrificing overall productivity.

Inventive Principle:

Principle #16Partial or excessive action

3Productivity

If data-dependent acquisition is performed based on real-time peptide ion identification, then efficient use of instrument time is achieved, but the complexity of the system increases

Engineering Contradiction:

Improveefficient use of instrument timeVSAvoidsystem complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent integrates database searching and peptide identification capabilities into the existing mass spectrometer control system. The same controller that manages instrument operation also performs or coordinates database searches, making the system multi-functional without adding separate dedicated hardware systems. This universal approach enables data-dependent acquisition based on real-time identification while minimizing the increase in overall system complexity.

Inventive Principle:

Principle #6Universality (Multi-functionality)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This approach enhances the throughput of mass spectrometry by ensuring timely peptide analysis, reducing sample waste, and allowing for more complete characterization of biological samples by avoiding prolonged search times.

Implementation Method 1

fragmenting the peptide ions to form product ions

Methodology Applied

Scientific EffectIon fragmentation:

Implementation Method 2

mass analyzing the product ions to acquire a product ion spectrum

Methodology Applied

Scientific EffectMass analysis:

Data Source

PatentUS11879897B2Operating a mass spectrometer utilizing mass spectral database search

Publication Date: 2024.01.23 THERMO FINNIGAN LLC

AI summary

Real-time search (RTS) for mass spectrometry is described. In one aspect, a mass spectrometer can identify a candidate peptide for a product ion spectrum by searching a mass spectral database. While executing the search of the mass spectral database, the elapsed search time can be monitored. If the elapsed search time of the identification of the candidate peptide is completed before reaching a maximum value, then the mass spectrometer can perform further actions.