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Method for evaluating quality of proteomics mass spectrum data

A technology of mass spectrometry data and proteomics, which is applied in the field of evaluating the quality of proteomics mass spectrometry data, can solve the problems of not being able to display the influencing factors of mass spectrometry data, time-consuming and labor-intensive analysis of mass spectrometry identification, etc.

Pending Publication Date: 2021-02-26
BEIHANG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

This method is not only time-consuming and labor-intensive, but more importantly, because the sampling inspection is extremely accidental, the results of this inspection cannot correctly reflect the shortcomings of the researcher's mass spectrometry experiment.
At the same time, manual analysis cannot show the quality of all mass spectrometry data influencing factors, so it may not correctly reflect the shortcomings of researchers' mass spectrometry experiments
At present, there is no similar method to automate the analysis of mass spectrometry data quality, and the factors affecting mass spectrometry data quality
Similar methods are mostly used to analyze the identification results of mass spectrometry in retrieval, but there is no method to analyze the quality of mass spectrometry identification results

Method used

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  • Method for evaluating quality of proteomics mass spectrum data
  • Method for evaluating quality of proteomics mass spectrum data
  • Method for evaluating quality of proteomics mass spectrum data

Examples

Experimental program
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Embodiment 1

[0075]The data comes from the article "Performance Evaluation of the Q Exactive HF X for Shotgun Proteomics" published in the "Journal of Proteome Research" in 2018. Example 1 uses the resolution set by the author of this article to be 15000, and the mass spectrometer QEHFX is used to analyze The resulting dataset for sample identification. First, the user loads the mass spectrum data, and extracts and calculates the actual data of the item corresponding to the required secondary scoring result. According to the scoring rules and actual data shown in Table 1, each secondary scoring result can be calculated. As shown in Table 2, 1.1 Peptide identification results, in the user data, 43052.81 peptides were identified per hour by mass spectrometry, and the linear scoring standard for item 1.1 is 5 points for mass spectrometry identification of more than 35,000 peptides per hour. 1 point for identifying less than 10,000 peptides. Obviously, the number of peptide identifications i...

Embodiment 2

[0081] The two datasets used in this embodiment are from the article "Performance Evaluation of the Q Exactive HF X for ShotgunProteomics" published in the "Journal of ProteomeResearch" in 2018. Dataset 1 is the dataset used in Example 1. Dataset 2 is the data set obtained by identifying the samples with the mass spectrometer QEHF (data set 1 is QEHFX) with the resolution set to 15000 by the author of this paper. Similarly, the two data sets were evaluated by the same method as in Example 1, and the inventors made a comparative analysis of the evaluation results.

[0082] First, if Figure 6 Shown: the data set 2 represented by the dotted line, the number of identified peptides is much higher than that of the data set 1 represented by the solid line, it can be seen that the quality of the mass spectrometry data of the data set 2 is higher than that of the data set episode 1.

[0083] In terms of the number of secondary spectrum acquisitions, data set 1 is much higher than da...

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Abstract

The invention discloses a method for evaluating the quality of proteomics mass spectrum data, and the method comprises the steps: carrying out the scoring of mass spectrum data obtained through testing, so as to obtain a first-level scoring result which comprises an identification result score, a second-level spectrum collection number score, a second-level spectrum utilization rate score and a second-level spectrum quality score; and taking the average score of the identification result score, the secondary spectrum acquisition number score, the secondary spectrum utilization rate score and the secondary spectrum quality score as the total score of the mass spectrum experiment. By analyzing most influence factors of mass spectrum experiment data obtained through experiments, each collected spectrogram and data of each identified peptide fragment in a mass spectrum experiment can be extracted for overall inspection, and sampling detection is not used. Therefore, the method can be usedto comprehensively, accurately, objectively and conveniently display the quality of each influence factor of the mass spectrum experiment data quality for the user, help the user to improve the experiment, and further promote the clinical application of the mass spectrum method.

Description

technical field [0001] The invention relates to the technical fields of biotechnology and proteomics, in particular to a method for evaluating the quality of proteomics mass spectrometry data. Background technique [0002] As an important method for bottom-up proteomics research in recent years, HPLC-MS method discovers protein markers of diseases or drugs by exploring protein components in biological cells or tissues, and studies molecular signaling pathways under different mechanisms or different Molecular interactions. Researchers judge the protein type and content contained in the sample according to the MS identification results, and draw conclusions by comparing different samples. In general, a large number of peptides and protein groups contained in the identification results can prove the quality of the experimental data and the quality of the HPLC-MS experiment. However, this method cannot judge the cause of high or low mass spectrometry data: that is, although re...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N33/68G01N27/62
CPCG01N33/6848G01N27/62
Inventor 刘超吴利则宫鹏云郭一洁李威铮汤敏
Owner BEIHANG UNIV