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Proteome mass spectrometric data processing method and device

A technology of proteome and mass spectrometry data, applied in the field of bioinformatics, can solve the problems of unreliable results, result differences, normalization, removal of batch effect differences, calculation and selection methods without consistent standards, etc.

Inactive Publication Date: 2020-10-20
苏州扇贝生物科技有限公司
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Problems solved by technology

[0005] However, the current proteome mass spectrometry data processing methods are diverse, and there is no consistent standard for normalization, batch effect removal, and difference calculation selection methods, which leads to different results obtained under different processing conditions for the same set of data. difference, so the unreliability of the results due to calculation errors is undoubtedly a pity

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  • Proteome mass spectrometric data processing method and device
  • Proteome mass spectrometric data processing method and device
  • Proteome mass spectrometric data processing method and device

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[0136] 1. Data preparation

[0137] The input files accepted by the present invention are off-machine data of proteome mass spectrometry (the name of the protein must be in the official standard gene symbol format) and parameter files.

[0138] 1.1 The proteome mass spectrometry data are as follows (the example is the proteome data of Escherichia coli in different culture media):

[0139]

[0140] 1.2 Run parameter input (all characters are English characters):

[0141] project_name = "Proteome_test";

[0142] project_dir=" / home / test / Proteome";

[0143] KEGG_enrichment = "eco";

[0144] GO_enrichment="org.EcSakai.eg.db";

[0145] norm_method="loess";

[0146] runDifferential = TRUE;

[0147] enrichment_qval = 0.05;

[0148] DEG_logFC = 1;

[0149] DEG_qval = 0.05;

[0150] …

[0151] 2. Data preprocessing

[0152] Handle missing values, perform the first overall quality analysis on the original data, and then perform LOESS normalization processing on the proteomi...

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Abstract

The invention provides a proteome mass spectrum data processing method. The method at least comprises the following steps: acquiring offline data and a parameter file of proteome mass spectrum; performing missing value processing on the offline data of proteome mass spectrometry; S2, performing normalization processing on the data obtained in the step S2, and then performing standardized conversion; and S4, performing batch effect correction on the data obtained in the step S3 according to batch information in the parameter file to obtain proteome mass spectrum data. The invention discloses the proteome mass spectrometric data processing method and device, the change of protein expression under different experimental conditions can be reflected more accurately, and then through enrichmentanalysis based on hyper-geometric distribution, different biological functions and biological pathways of different experimental groups under different experimental treatments are obtained, so that the method has important significance in combined analysis with other omics data.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a proteome mass spectrometry data processing method and device. Background technique [0002] The proteome is the sum of all protein species in a single set of organisms or cells. Proteomics essentially refers to the study of protein characteristics on a large-scale level, including protein expression levels, post-translational modifications, protein-protein interactions, etc., thereby obtaining information about disease occurrence, cell metabolism, etc. at the protein level. A holistic and comprehensive understanding of the process. It is a mature and effective tool for systematically studying biological laws and mechanisms. According to different research purposes, proteomics can be divided into expression proteomics, structural proteomics and functional proteomics. [0003] Quantitative proteomics refers to mass spectrometry detection of specific known proteins, rather than fu...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N33/68G16B40/30
CPCG01N33/6848G16B40/30
Inventor 桑运霞孙天拥刘强左冰云王凤
Owner 苏州扇贝生物科技有限公司
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