An automated proteomics mass spectrometer operation and maintenance and data quality control system

Abstract

The present invention provides an automated proteomics mass spectrometer operation and maintenance and data quality control system, including: a mass spectrometer computer terminal, which is used to collect mass spectrometer files of the instrument and obtain monitoring files of the instrument; a database search computer terminal, which is used to search the mass spectrometer files, analyze and process them to obtain database search result information files and quality control files; a message sending terminal, which obtains database search result information files, quality control files, and monitoring files, and sends them to corresponding personnel. The present invention sets the mass spectrometer computer terminal to automatically collect mass spectrometer files, and simultaneously obtains the status information of the instrument, then searches the database and processes the data through the database search computer terminal, and finally sends the database search result information files, quality control files, and monitoring files to corresponding personnel through the message sending terminal, so as to realize the automated processing of the database search process and the automatic extraction and sending of the database search results, thereby reducing manual intervention.

Description

Technical Field

[0001] The present invention relates to the technical field of protein databases, and in particular to an automated proteome mass spectrometer operation and maintenance and data quality control system. Background Art

[0002] The exploration of disease mechanisms and precision medicine rely on the promotion of a series of omics technologies such as proteomics and metabolomics. Through the data collection and analysis of large cohorts and specific subtype disease samples, the causes of diseases and treatment targets are sought. In recent years, the research and exploration of various clinical problems through proteomics has progressed rapidly. With the rapid development of proteomics data collection instruments, fast data processing methods and quality monitoring of omics data have become methods that urgently need to be solved. At present, there is still a lot of manual intervention in the process of mass spectrometry engineers processing data, such as manual copying from mass spectrometry computers to search database computers / search database clusters, manual setting of search database parameters, and manual viewing of search database results.

[0003] There are many mainstream proteomics data processing software. There are big differences in the search result files of different search software. Some search software is not friendly to the viewing of mass spectrometry file search results. The existing process software is mainly based on server clusters. The search software does not cover all aspects and small laboratories lack the conditions for deployment. Therefore, there is still a lack of automated processing software for data collection, data search, search result post-processing, quality control result monitoring and other processes. Summary of the invention

[0004] In order to overcome the problems existing in the prior art, the object of the present invention is to provide an automated proteomics mass spectrometer operation and maintenance and data quality control system, which can realize automated processing of data acquisition, database search result post-processing, and quality control result monitoring.

[0005] To achieve the above object, the present invention adopts the following technical solutions:

[0006] An automated proteomics mass spectrometer operation and maintenance and data quality control system, comprising:

[0007] Mass spectrometer computer terminal, used to collect the instrument's mass spectrometer files and obtain the instrument's monitoring files;

[0008] The computer terminal for searching the database is used to search and analyze the mass spectrometry files to obtain the search result information files and quality control files;

[0009] The message sending end obtains the search result information file, quality control file, and monitoring file, and sends them to the corresponding personnel.

[0010] As a further improvement of the present invention, the mass spectrometer computer determines the collection status of the mass spectrometer file according to the scanning interval time, the threshold value for ignoring the scanning file, the judgment interval time, and the column cleaning time.

[0011] As a further improvement of the present invention, the mass spectrometer computer determines the collection status of the mass spectrometer file according to the scanning interval time, the threshold value of ignoring the scanning file, the judgment interval time, and the chromatographic column cleaning time, including the steps of:

[0012] 1-1. Scan and find unprocessed mass spectrometry files. If the size of the mass spectrometry file is smaller than the threshold for ignoring scanned files, wait for another scan interval and continue to judge, and repeat step 1-1.

[0013] 1-2. If the size of the mass spectrum file is greater than the threshold for ignoring scanned files, the size of the mass spectrum file is acquired cyclically and it is determined whether the size of the acquired mass spectrum file changes during the adjacent scan intervals. If so, step 1-2 is continued. If not, step 1-3 is executed.

[0014] 1-3. Considering the impact of the chromatographic column cleaning time on data integrity, after step 1-2, wait for the chromatographic column cleaning time, and repeatedly determine whether the size of the mass spectrum file has changed. If there is no change, the data acquisition is considered complete and the acquisition has been stopped. The data transmission is automatically performed and the mass spectrum file name is recorded in the document. Then, return to step 1-1 and restart monitoring the newly generated mass spectrum file and other unrecorded mass spectrum files. If the file size changes, return to step 1-2;

[0015] 1-4. If the size of the mass spectrum file is less than the threshold value for ignoring scanned files, repeat the steps of waiting for another scan interval and then continuing to determine whether the file size has changed for several times. If the size of the mass spectrum file has not changed, it is considered that the acquisition of the mass spectrum file is interrupted, and the transmission of the mass spectrum file is ignored and the file name is recorded in the document. Return to step 1-1 and restart monitoring the newly generated mass spectrum file and other unrecorded mass spectrum files;

[0016] 1-5. After all processes are executed correctly, the file name successfully transferred to the search computer will be recorded in a specific file. The user can realize the secondary automatic search of mass spectrometry files by modifying the content of the specific file.

[0017] As a further improvement of the present invention, the mass spectrometer computer obtains the status information of the instrument from the monitoring instrument log file through the Socket socket method;

[0018] The mass spectrometer computer terminal provides an interface for users to modify the extraction rules of the mass spectrometer instrument log monitoring file;

[0019] The computer end of the message sending obtains the status information of the above instruments through the Socket socket method.

[0020] As a further improvement of the present invention, on the computer side of the database search, a visual custom setting of the database search parameters is provided through the QFileDialog function; the parallel operation of different database search software or the same database search software is supported through the QThread thread class module, and different parallel interfaces are bound to different data receiving port parameters to receive data from different projects / sources; data is received from the client via the Socket socket method, allowing multiple clients to transmit in parallel to the same data receiving port.

[0021] As a further improvement of the present invention, the database search computer end extracts information from the database search result file of the completed database search and actively summarizes it to the message sending end through the Socket socket method; the database search computer end processes the database search result file to obtain identification number information reflecting the mass spectrum file acquisition quality, information reflecting the liquid phase system state, and information reflecting the mass spectrometer instrument state, and performs abnormal value judgment on the identification number information reflecting the mass spectrum file acquisition quality, the information reflecting the liquid phase system state, and the information reflecting the mass spectrometer instrument state.

[0022] As a further improvement of the present invention, the quality control reference result parameter files are added in batches on the database search computer and corresponding labels are generated, and the information of the new files is judged to be abnormal with the added quality control reference results as the reference standard;

[0023] The computer end of the library search scans the file name of the mass spectrum file to determine whether to perform quality control of the library search results;

[0024] The computer end of the search library compares the content of the existing quality control file with the recorded quality control results of the corresponding label. If the judgment result is abnormal, the abnormal value information and other quality control content will be sent to the message sending end for sending to the corresponding personnel. If the judgment result is normal, only the quality control content will be sent to the message sending end for sending to the corresponding personnel.

[0025] As a further improvement of the present invention, the database search computer compares the existing quality control file with the recorded quality control result. If the result is abnormal, the abnormal value information is sent to the message sending end to be sent to the corresponding personnel, including the steps of:

[0026] Determine whether the monitoring information extracted from the quality control file is within the reference data range. If all monitoring information is within the reference range, the instrument is considered normal.

[0027] If any monitoring information exceeds the reference range, the 1.5 times IQR interquartile range threshold method and the generalized extreme studentized deviation test methods are used to determine whether the monitoring information is an outlier. If an outlier exists, the outlier information is sent to the message sending end to be sent to the corresponding personnel.

[0028] As a further improvement of the present invention, the computer terminal of the database search connects to the original queue of the database search software through a visual interface to merge the database search results. The visual interface performs one-click processing on the quantitative expression matrix after preliminary processing according to the user's call;

[0029] The computer version of the search library supports queue merging and quantitative file processing of the search library, including the following steps:

[0030] The computer terminal of the search library triggers the filtering condition options for different search library software through the selected software button;

[0031] The computer end of the database search forms a process for processing the database search result file by selecting parameters;

[0032] The computer side of the search library performs the corresponding data processing process according to the processing flow selected by the user, and outputs the processing pictures of some process results according to the preset settings;

[0033] The computer-side data processing code for the search library is based on Python, and the selection of each parameter button is performed through pyqt5. The QThread thread class module supports the parallel operation of merging search results of different search software or merging search results of the same search software.

[0034] The computer side of the search library performs dimensionality reduction on the data and displays it using a point graph;

[0035] The computer side of the search database normalizes the samples and fills in missing values;

[0036] The computer version of the search library displays the changes before and after quantitative data processing.

[0037] As a further improvement of the present invention, the message sending end calls the itchat module to mobilize the WeChat interface to send the search result information file and the monitoring file; the message sending end calls the email module to send the search result information file and the monitoring file.

[0038] The beneficial effects of the present invention are: setting the mass spectrometry computer end for automatic collection of mass spectrometry files, acquiring the monitoring files of the instrument at the same time, then searching the library and processing the data through the library search computer end, and finally sending the result information files, quality control files, and monitoring files to the corresponding personnel through the message sending end library search, thereby realizing the automated processing of the library search process and the automatic extraction and sending of the library search results, reducing manual intervention and improving work efficiency. BRIEF DESCRIPTION OF THE DRAWINGS

[0039] The present invention is further described in detail below based on the accompanying drawings and embodiments.

[0040] Figure 1 It is a flowchart of searching the database for the prior art;

[0041] Figure 2The overall structure and process diagram of the automated proteomics mass spectrometer operation and maintenance and data quality control system of the present invention;

[0042] Figure 3 It is the main interface of the computer terminal running the database search described in the present invention;

[0043] Figure 4 It is the operating interface of the computer-side database search software of the present invention;

[0044] Figure 5 The computer-side single-needle search result sorting function of the database search described in the present invention;

[0045] Figure 6 The single-needle database search result quality control function of the database search computer terminal described in the present invention;

[0046] Figure 7 It is the merging function of the single-needle search results on the computer side of the search database described in the present invention;

[0047] Figure 8 The computer-side multi-data search result statistics function of the present invention is to merge multiple data into one;

[0048] Fig. 9 The computer-side search database queue merges the database search data processing interface described in the present invention;

[0049] Fig.10 It is the computer terminal operation interface of the mass spectrometer of the present invention;

[0050] Fig.11 A computer definition function for searching the mass spectrometer computer data base according to the present invention;

[0051] Fig.12 The mass spectrometer computer operation status monitoring function of the present invention;

[0052] Fig.13 Setting an interface for the message sending terminal of the present invention;

[0053] Fig.14 It is a message sending file directional sending setting interface in the message sending terminal of the present invention;

[0054] Fig.15 It is a message sending content setting interface in the message sending terminal of the present invention;

[0055] Fig.16 This is an example of setting the Spectronaut search parameter in the present invention;

[0056] Fig.17 This is the actual operation interface of Spectronaut automatic database search in the present invention;

[0057] Fig.18 This is an example of the parameter file of the present invention;

[0058] Fig.19 It is the setting interface of the mass spectrometer computer terminal of the present invention;

[0059] Fig. 20 It is the instrument status monitoring interface in the present invention;

[0060] Fig.21 A code for receiving result files in the present invention;

[0061] Fig. 22 It is the message sending main body interface in the message sending end implementation mode of the present invention;

[0062] Fig.23 It is a result / email-specific sending setting interface in the message sending end implementation mode of the present invention;

[0063] Fig.24 This is a message / mail content selection interface in the message sending end implementation mode of the present invention. DETAILED DESCRIPTION

[0064] In order to make the technical problems solved by the present invention, the technical solutions adopted and the technical effects achieved clearer, the technical solutions of the embodiments of the present invention are further described in detail below. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of them. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative work are within the scope of protection of the present invention.

[0065] like Figure 1 As shown, it is a schematic diagram of the process of searching a database in the prior art. It can be seen that the existing database searching process has a low degree of automation and requires a lot of human resources.

[0066] The present invention provides an automated proteomics mass spectrometer operation and maintenance and data quality control system, which can solve the above problems, such as Figure 2 As shown, it includes: a mass spectrometry computer terminal, a library search computer terminal and a message sending terminal; wherein, the mass spectrometry computer terminal is used to collect the mass spectrometry files of the instrument and obtain the monitoring files of the instrument; the library search computer terminal is used to search the mass spectrometry files, analyze and process them to obtain the library search result information files and quality control files; the message sending terminal obtains the library search result information files, quality control files and monitoring files, and sends them to the corresponding personnel.

[0067] Specifically, the mass spectrometer computer determines the acquisition status of the mass spectrometer file by monitoring the size changes of the new mass spectrometer file. The parameter files corresponding to the acquisition monitoring include: scanning interval time, ignoring scanning file threshold, judgment interval time, and chromatographic column cleaning time to determine the acquisition status of the mass spectrometer file. It should be noted that users can use the default settings or customize them by modifying the parameter files according to laboratory conditions.

[0068] Select one of the implementation scenarios for detailed description:

[0069] The acquisition status of the mass spectrometry file is determined according to the scanning interval, the threshold value of the scanned file to be ignored, the judgment interval, and the chromatographic column cleaning time. The size change of the newly appeared mass spectrometry file in the monitoring directory is cyclically scanned to determine whether the acquisition of the mass spectrometry file is completed. After the acquisition is completed, data transmission begins, including the following steps:

[0070] 1-1. Scan and find unprocessed mass spectrometry files (such as newly generated mass spectrometry files). If the size of the mass spectrometry files is smaller than the threshold for ignoring scanned files, wait for another scan interval and continue to judge, and repeat step 1-1.

[0071] 1-2. If the size of the mass spectrum file is greater than the threshold for ignoring scanned files, the size of the mass spectrum file is acquired cyclically to determine whether the size of the acquired mass spectrum file changes during the adjacent scan intervals. If so, continue to execute step 1-2. If not, execute step 1-3.

[0072] 1-3. Considering the impact of the chromatographic column cleaning time on data integrity, after step 1-2, wait for the chromatographic column cleaning time, and repeatedly determine whether the size of the mass spectrum file has changed. If there is no change, the data acquisition is considered complete and the acquisition has been stopped. The data transmission is automatically performed and the mass spectrum file name is recorded in the document. Then, return to step 1-1 and restart monitoring the newly generated mass spectrum file and other unrecorded mass spectrum files. If the file size changes, return to step 1-2;

[0073] 1-4. If the size of the mass spectrum file is less than the threshold for ignoring scanned files, repeat the steps of waiting for another scan interval and then continuing to determine whether the file size has changed for several times. If the size of the mass spectrum file has not changed, it is determined that the acquisition of the mass spectrum file is interrupted. Since the file has not been completely acquired, no subsequent processing will be performed, that is, the transmission of the file is ignored and the file name is recorded in the document. Return to step 1-1 and restart monitoring of the newly generated mass spectrum file and other unrecorded mass spectrum files.

[0074] 1-5. Execute all the processes correctly, and the file name successfully transferred to the search computer will be recorded in a specific file. The user can directly modify the content of the specific file to realize the secondary automatic search of the mass spectrometry file.

[0075] The mass spectrometer computer obtains instrument operation information by cyclically monitoring the instrument log file. The message sending computer obtains instrument status information through Socket. The mass spectrometer computer can monitor the status of three mainstream mass spectrometers: Thermo, Bruker, and SCIEX. For example, the Thermo-E480 instrument monitors the log file content in the C:\ProgramData\Thermo\Exploris\Log folder, and the newly added [Type=error] annotation content is the instrument abnormal information file. The Bruker-timsTOF instrument monitors the CompassHyStarErrorLogbook.log log file to obtain the corresponding instrument status information, which is marked as . The SCIEX instrument monitors the Shimadzu liquid phase log file or instrument operation status information, and the abnormal information is marked as FATAL.

[0076] The mass spectrometer computer terminal provides an interface for users to modify the extraction rules of the mass spectrometer instrument log monitoring file; users can modify the extraction rules to obtain the desired content according to the changes in text information type or text content, and the extraction rules are identified by a third-party python module.

[0077] like Figure 3 As shown in the figure, it is one of the interfaces provided by the mass spectrometer computer. Through this interface, the parameter files required for library search are set. Different library search software have different library search interfaces. The mass spectrometer computer supports MaxQuant, ProteomeDiscoverer, and Spectronaut. The use of MaxQuant software requires the installation of Mono software in advance. Users can run the program interface supporting different library search software by clicking different buttons, and support the parallel operation of the program, such as Figure 4 shown.

[0078] When the acquisition of a new mass spectrometry file is completed or the instrument status is abnormal, the mass spectrometry computer completes the directional transmission of data and instrument status information files through the Socket socket. The data transmission computer and the instrument status message receiving computer are selected from the interface drop-down menu, and the Socket transmission port is used to distinguish files transmitted to the same computer; the data transmission computer and the status message file receiving computer can be added, deleted, and modified through the interface. They are composed of custom labels and the search computer IP, such as MSG:192.168.100.100. When the user selects the MSG computer, it decides to send data to the computer with the IP address 192.168.100.100.

[0079] like Figure 10-12As shown, the mass spectrometer computer terminal supports three types of database search software corresponding to the database search computer terminal. The parameter file comes from the file generated by the data receiving folder of the database search computer terminal. The parameter file executed by the Proteome Discoverer script must be directly generated by the Proteome Discoverer software; the mass spectrometer computer terminal can perform integrity detection on the mass spectrometer file being collected, considering the file size changes and data acquisition process during the acquisition process, the text change scanning time, and the data acquisition interval time can all be set by the parameter file; the mass spectrometer computer terminal also defines the data receiving computer through IP, supports IP address replacement, and database search computer terminal alias definition; the mass spectrometer computer terminal supports monitoring of the mass spectrometer instrument status and liquid phase system status by monitoring mass spectrometer log files or liquid phase files.

[0080] The computer side of the search library uses the PyQt5 module to realize the visualization of the interface, and provides the visualization and customization of the search parameters through the QFileDialog function. On the visualization interface, users can realize the customization of the search software, search software version, data storage location, search result location, etc.; the computer side of the search library supports the parallel operation of automatic search of the same search software or different search software through the QThread thread class module. The computer side of the search library is equipped with multiple data receiving terminals. Different parallel interfaces are bound to different data receiving port parameters to receive data from different projects / sources. The bound content can be recorded in the database. Users can query the port number to reproduce the set search parameters, so that the computer side of the search library can support the same search workstation to automatically execute customized search requirements for different projects; data reception receives client data by Socket socket, allowing multiple clients to transmit to the same data receiving port in parallel.

[0081] After the search parameters are run, the search computer data receiving folder generates a search parameter file used by the client. Different port numbers execute different search software. Customized data search can be achieved by setting up multiple search programs in parallel.

[0082] By setting up multiple data receiving ends on the computer side of the database search, the data receiving port number and other parameter bindings can be added to the software database. Users can query the database through the port number to reproduce the port binding parameters. The port and parameter information in the database also supports addition and modification. The computer side of the database search can independently determine whether the data reception is completed. When the transmission is interrupted or there is no database search parameter file, it will actively interrupt subsequent database search tasks. Under normal circumstances, the command line running code of the database search program is executed by calling the received specific parameter file.

[0083] The computer terminal of the database search stores a result extraction program. The scheduled scanning result extraction program automatically extracts information from the database search result files of the completed database search and actively summarizes it to the message sending terminal through the Socket socket. The scanning frequency can be set by the user; the result extraction program processes the database search result files such as proteins, peptides, spectra, parent ions, etc., and obtains the identification number information such as proteins, peptides, spectra, points, peak capacity, signal intensity, etc. that reflect the quality of mass spectrometry file acquisition, and the peak width, mass axis deviation, IRT and other internal standard peptide retention time that reflect the state of the liquid phase system. After excluding outliers from the peak width and mass axis deviation data through the 1.5 times IQR interquartile range threshold, the 75% digit, 50% digit, and 25% digit position information of peak width, retention time, etc. are provided to truly reflect the data information.

[0084] The computer terminal of the search library supports the extraction of quality control information from the newly generated quality control file search results based on the existing results by selecting the scan folder and software result type. For example Figure 5 shown.

[0085] The interface of the computer terminal of the search library supports batch adding of quality control reference result parameter files and generating corresponding labels; if the quality control result monitoring is turned on, the computer terminal of the search library will scan the file name of the mass spectrum file to determine whether to perform quality control result monitoring; the computer terminal of the search library will compare the existing quality control file with the recorded quality control results. If the result is abnormal, the abnormal value information will be sent to the message sending end to send to the corresponding personnel. The specific steps include:

[0086] Determine whether the monitoring information extracted from the quality control file (such as the number of proteins and peptides, mass axis deviation, peak width, signal intensity, etc.) is within the reference data range. If all the monitoring information is within the reference range, the instrument is considered normal.

[0087] If any monitoring information exceeds the reference range, the 1.5 times IQR interquartile range threshold method and GESD (Generalized Extreme Studentized Deviate) test method are used to determine whether the monitoring information is an outlier. If so, the outlier information is sent to the message sending end to be sent to the corresponding personnel. IQR is the interquartile range, which is calculated by subtracting the first quartile from the third quartile. The GESD test does not require the number of outliers to be specified in advance, and the outliers theoretically existing in the data set can be independently determined (for details of GESD, please refer to Rosner, Bernard (May 1983), Percentage Points for a Generalized ESD Many-Outlier Procedure, Technometrics, 25 (2), pp. 165-172.).

[0088] Based on the settings of the above steps, according to the user input of the existing reference quality control result file, the library search computer can generate monitoring information corresponding to a specific type of quality control file, so as to monitor whether the library search results of the newly generated mass spectrum file meet the preset rules, such as Figure 6 shown.

[0089] The computer terminal of the search library supports multiple selections to realize the quality control file monitoring of multiple search library types. At the same time, it also provides the combined statistical code of the single needle search library results to facilitate the statistics of single needle results, such as Figure 7 shown.

[0090] The computer version of the search library uses PyQts5 to implement a visualization interface. The visualization interface connects to the original queue of the search library software (such as MaxQuant, MsFragger, Spectronaut) to merge the search results. The visualization interface performs one-click processing on the quantitative expression matrix after preliminary processing according to the user's call.

[0091] The computer version of the search library supports queue merging and quantitative file processing of the search library, including the following steps:

[0092] The computer terminal of the search library triggers the filtering condition options for different search library software through the selected software button;

[0093] The computer terminal of the database search forms a process for processing the database search result files by selecting parameters such as missing value processing, normalization processing, data dimension reduction, and column name modification files;

[0094] The computer side of the search library performs the corresponding data processing process according to the processing flow selected by the user, and outputs the processing pictures of some process results according to the preset settings;

[0095] The computer-side data processing code for the search library is completed based on python, and pyqt5 is used to select various parameter buttons. The QThread thread class module supports the parallel operation of merging search results of different search software or merging search results of the same search software.

[0096] In the specific use process, after the user enters or selects the original result file location, output file location, and group renamed file through the dialog box supported by QFileDialog, the one-click processing of queue merging data can be realized through the default parameters. The default parameters are Intensity for quantitative data, median normalization method, global minimum filling, and PCA data dimensionality reduction display. In addition, the computer end of the search library allows the call of the visualization interface to perform one-click processing on the quantitative expression matrix that has been preliminarily processed by other software. It should be noted that this visualization interface does not include certain specific software parameters: targeted parameter options are provided for different software, such as the PG.NrOfStrippedSequencesIdentified (Experiment-wide) parameter of the Spectronaut software, such as the Protein Probability parameter of the MsFragger software, and the Reverse, Potential contaminant, LFQ, and iBAQ parameters of the MaxQuant software.

[0097] The computer version of the search library supports queue merging and search library quantitative file processing, supports KNN filling based on Python modules such as umap and sklearn, PCA, Umap, and T-SNE data dimensionality reduction methods, and supports Python function-defined missing value global minimum filling, median normalization, Quantile normalization, mean normalization and other operations.

[0098] like Figure 8 and Fig. 9 As shown in the figure, the computer terminal of the database search has the function of queue result processing: it can support the basic information statistics of multi-sample queue search results of three mainstream database search software, provide protein and peptide identification information, missed cutting information, mass axis deviation information, etc., and support the original search results of MaxQuant / MsFragger / Spectronaut software; additionally support matrix type input results generated by other software such as DIA-NN; provide protein screening of omics matrix, and different software search results support specific screening conditions, such as the screening of marker information such as Reverse / Potential contaminant / Uniquepeptides number in MaxQuant quantitative matrix.

[0099] The computer side of the search library performs dimensionality reduction processing on the data and displays it with a dot plot; for example, converting an N*M (the number of columns M is generally in the range of 200-12000) data list into an N*2 or N*3 data list and using a two-dimensional or three-dimensional dot plot for intuitive display; this method is often used to determine whether there are avoidable human factors or instrument factors, and whether the sample groups are distinguishable. PCA, UMAP, and t-SNE are all unsupervised dimensionality reduction algorithms, among which PCA is a linear dimensionality reduction method that performs an orthogonal transformation on the data in the original feature space to obtain a new low-dimensional feature space. t-SNE and UMAP are nonlinear dimensionality reduction methods that attempt to preserve the local structure between data points in a low-dimensional space while ignoring the global structure. For the principle of t-SNE data dimensionality reduction, please refer to Laurens, VDM, & Hinton, G.. (2008). Visualizing data using t-sne. Journal of Machine Learning Research, 9(2605), 2579-2605., and for the principle of UMAP data dimensionality reduction, please refer to Mcinnes, L., & Healy, J.. (2018). Umap: uniform manifold approximation and projection for dimension reduction. The Journal of Open Source Software, 3(29), 861.

[0100] The computer side of the search library normalizes the samples and fills in missing values; normalization makes the data between samples comparable and corrects possible sample amount errors. The software can provide three data normalization methods: median normalization, mean normalization, and Quantile method. Median normalization is to divide the data in the column by the non-zero median of the column, and mean normalization is to divide the data in the column by the non-zero mean of the column. Both assume that the median and mean data only change with the sample amount rather than the number of identified proteins. The Quantile method combines the rank of the data sorting with the quantitative value of the data, and sets the same quantitative value for the same sorting position. The quantitative value comes from the mean of the quantitative value of the original sorting position of each sample. The Quantile principle refers to Roger Koenker. (2005). Quantile regression. Cambridge University Press. When the missing value is formed in the quantitative data table, the quantitative information of the protein in the sample cannot be confirmed. The reason may be due to the limitation of the quantitative software or the protein content is lower than the detection limit. Based on the above understanding, the software provides three methods to fill the missing values: replacing the missing value with the global minimum value of the table, replacing the missing value with the Quantile method based on the missing value being 0, and inferring the missing value based on the KNN algorithm combined with adjacent data. The principle of KNN refers to Cover, TM, & Hart, PE. (1953). Nearest neighbor pattern classification. IEEE Trans. inf. theory, 13 (1), 21-27.

[0101] The computer side of the search library displays quantitative data, such as heat maps, correlation graphs, CV graphs, quantitative range box plots, data dimensionality reduction results, and results before and after normalization based on python modules such as plotnine, matplotlib, and seaborn.

[0102] The message sending end receives the search result information file, quality control file and instrument status information of the mass spectrometer computer end through the Socket socket method. In the message sending end, a graphical interface is set up for users to select the sending method and content. By judging whether the file name meets the sending rules, the object to which the content is sent is determined. By judging the file name type, the file content is personalized and sent. Specific content.

[0103] As an example, Fig.13As shown, the message sender can use WeChat to send files. The message sender calls the itchat module to mobilize the WeChat interface to send messages. Itchat is a third-party library for the development of WeChat personal accounts. It can realize WeChat login, receiving and sending messages, obtaining friend lists and other functions. The message object sent by WeChat is obtained through the graphical interface, and the message is sent through the friend list. The content of the message is the instrument monitoring file or quality control file result. Some optional content can be customized through the graphical interface to choose whether to send. The file type of the message sent can be adjusted through the mass spectrometer and engineer interface project options to realize the functions of selecting specific types of result files and specifying the recipient. The interface is as follows Fig.14 The message sending and receiving can be adjusted through the software interface to adjust some optional contents. The interface is as follows Fig.15 shown.

[0104] As another example, Fig.13 As shown in the figure, the message sender can send files by email. The message sender calls the email module to send the corresponding content, and completes the email content through the emai module, that is, the addition of instrument monitoring files or quality control file results. Some optional content can be customized in the graphical interface to select whether to send, and the email address of the object to be sent can be added in the graphical interface. The file type of the message can be adjusted through the project options of the mass spectrometer and engineer interface to realize the functions of selecting specific types of result files and specifying the recipient. The interface is as follows Fig.14 The message sending and receiving can be adjusted through the software interface to adjust some optional contents. The interface is as follows Fig.15 shown.

[0105] In addition, you can also set the message sending time period in the message sending terminal. Users can define the time period for message sending. The files received during this period will be resent during the allowed time period. The search computer terminal can be run on the same computer as the message sending terminal or on different computers. The interface is as follows: Fig.12 shown.

[0106] Next, the present invention is further explained in conjunction with the specific implementation process, as follows:

[0107] The test mass spectrometers are sourced from three mainstream mass spectrometer manufacturers, namely Thermo's E480 / Eclipse mass spectrometer, Bruker's tims-Pro / SCP mass spectrometer, and SCIEX's 5500 / 6600 / 7600 mass spectrometer. The mass spectrometer computer is purchased as a mass spectrometer-equipped computer, and the database search computer is a workstation computer. The operating system is Windows system. To run the database search computer, the Windows system firewall must be closed to allow data transmission.

[0108] Taking Spectronaut software as an example, after setting the sample parameters, the preset process can be realized, including automatic library search, automatic statistics, real-time sending of library search results, sample quality control, instrument status monitoring and other functions.

[0109] 1. First, call the Spectronaut search library setting interface. When the interface is opened, users can use the port number to reproduce the parameters or use the button to choose whether to overwrite the original parameters. The software supports running different search library parameters for different port numbers, such as Fig.16 , Fig.17 As shown;

[0110] 2. Obtain the parameters generated by the software in the Result_Dir folder. The parameter file needs to be transferred to the mass spectrometer computer for use. Fig.18 As shown;

[0111] 3. The Run_Port port number on the mass spectrometer computer must be consistent with the port number required to execute the database search parameters. Set the temporary data folder Data Storge and the data file generation folder Acquisition Dir. After loading the corresponding parameter file, you can run it. Fig.19 As shown;

[0112] 4. Set the data sending computer-MSG, sending port, instrument type, instrument abbreviation and other information on the mass spectrometer computer. Different types of instruments monitor different types of files. After the settings are completed, just run it. Fig. 20 As shown;

[0113] 5. Monitor the computer where the information is sent (the computer corresponding to MSG), start the result file receiving program and the message sending program. The message sending program supports the sending of specific messages and the selection of sending message options, etc.

[0114] In summary, compared with the traditional data copying and data search processes implemented by engineers, the present invention realizes the automation of processes such as data collection, data result extraction, data result quality control, and instrument status monitoring; the automated process of the present invention significantly improves the output efficiency of data result information and optimizes the utilization of computing resources; the present invention additionally provides instrument status monitoring, and engineers can quickly obtain mass spectrometry results and instrument status information through email and WeChat tools.

[0115] The technical principle of the present invention is described above in conjunction with specific embodiments. These descriptions are only for explaining the principle of the present invention and cannot be interpreted as limiting the scope of protection of the present invention in any way. Based on the explanations herein, those skilled in the art can associate other specific implementations of the present invention without paying creative labor, and these methods will fall within the scope of protection of the present invention.

Claims

1. An automated proteomics mass spectrometer operation and maintenance and data quality control system, characterized in that: include: Mass spectrometer computer terminal, used to collect the instrument's mass spectrometer files and obtain the instrument's monitoring files; The computer terminal for searching the database is used to search and analyze the mass spectrometry files to obtain the search result information files and quality control files; The message sending end obtains the search result information file, quality control file, and monitoring file, and sends them to the corresponding personnel; The mass spectrometer computer determines the collection status of the mass spectrometer file based on the scanning interval, the threshold for ignoring scanning files, the judgment interval, and the chromatographic column cleaning time; The mass spectrometer computer determines the collection status of the mass spectrometer file according to the scanning interval time, the threshold value of ignoring the scanning file, the judgment interval time, and the chromatographic column cleaning time, including the following steps: 1-1. Scan and find unprocessed mass spectrometry files. If the size of the mass spectrometry file is smaller than the threshold for ignoring scanned files, wait for another scan interval and continue to judge, and repeat step 1-1. 1-2. If the size of the mass spectrum file is greater than the threshold for ignoring scanned files, the size of the mass spectrum file is acquired cyclically and it is determined whether the size of the acquired mass spectrum file changes during the adjacent scan intervals. If so, step 1-2 is continued. If not, step 1-3 is executed. 1-3. Considering the impact of the chromatographic column cleaning time on data integrity, after step 1-2, wait for the chromatographic column cleaning time, and repeatedly determine whether the size of the mass spectrum file has changed. If there is no change, the data acquisition is considered complete and the acquisition has been stopped. The data transmission is automatically performed and the mass spectrum file name is recorded in the document. Then, return to step 1-1 and restart monitoring the newly generated mass spectrum file and other unrecorded mass spectrum files. If the file size changes, return to step 1-2; 1-4. If the size of the mass spectrum file is less than the threshold value for ignoring scanned files, repeat the steps of waiting for another scan interval and then continuing to determine whether the file size has changed for several times. If the size of the mass spectrum file has not changed, it is considered that the acquisition of the mass spectrum file is interrupted, and the transmission of the mass spectrum file is ignored and the file name is recorded in the document. Return to step 1-1 and restart monitoring the newly generated mass spectrum file and other unrecorded mass spectrum files; 1-5. After all processes are executed correctly, the file name successfully transferred to the search computer will be recorded in a specific file. The user can realize the secondary automatic search of mass spectrometry files by modifying the content of the specific file.

2. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: The mass spectrometer computer obtains the instrument status information from the monitoring instrument log file through the Socket socket method; The mass spectrometer computer terminal provides an interface for users to modify the extraction rules of the mass spectrometer instrument log monitoring file; The computer end of the message sending obtains the status information of the above instruments through the Socket socket method.

3. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: On the computer side of the database search, the QFileDialog function provides visual customization of the database search parameters; the QThread thread class module supports the parallel operation of different database search software or the same database search software, and different parallel interfaces are bound to different data receiving port parameters to receive data from different projects / sources; Data reception receives client data through Socket, allowing multiple clients to transmit to the same data receiving port in parallel.

4. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: The computer end for searching the database extracts information from the search result files of the completed database search and actively summarizes them to the message sending end through the Socket socket method; the computer end for searching the database processes the search result files to obtain the identification number information reflecting the acquisition quality of the mass spectrometry file, the information reflecting the status of the liquid phase system, and the information reflecting the status of the mass spectrometry instrument, and makes abnormal value judgments on the identification number information reflecting the acquisition quality of the mass spectrometry file, the information reflecting the status of the liquid phase system, and the information reflecting the status of the mass spectrometry instrument.

5. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: Batch add quality control reference result parameter files on the search library computer and generate corresponding labels, and use the added quality control reference results as the reference standard to judge the abnormal status of the information of the new files; The computer end of the library search scans the file name of the mass spectrum file to determine whether to perform quality control of the library search results; The computer end of the search library compares the content of the existing quality control file with the recorded quality control results of the corresponding label. If the judgment result is abnormal, the abnormal value information and other quality control content will be sent to the message sending end for sending to the corresponding personnel. If the judgment result is normal, only the quality control content will be sent to the message sending end for sending to the corresponding personnel.

6. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: The search database computer compares the existing quality control files with the recorded quality control results. If the result is judged to be abnormal, the abnormal value information is sent to the message sending end to be sent to the corresponding personnel, including the following steps: Determine whether the monitoring information extracted from the quality control file is within the reference data range. If all monitoring information is within the reference range, the instrument is considered normal. If any monitoring information exceeds the reference range, the 1.5 times IQR interquartile range threshold method and the generalized extreme studentized deviation test methods are used to determine whether the monitoring information is an outlier. If an outlier exists, the outlier information is sent to the message sending end to be sent to the corresponding personnel.

7. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: The computer terminal of the database search connects to the original queue of the database search software through a visual interface to merge the database search results. The visual interface performs one-click processing on the quantitative expression matrix after preliminary processing according to the user's call; The computer version of the search library supports queue merging and quantitative file processing of the search library, including the following steps: The computer terminal of the search library triggers the filtering condition options for different search library software through the selected software button; The computer end of the database search forms a process for processing the database search result file by selecting parameters; The computer side of the search library performs the corresponding data processing process according to the processing flow selected by the user, and outputs the processing pictures of some process results according to the preset settings; The computer-side data processing code for the search library is based on Python, and the selection of each parameter button is performed through pyqt5. The QThread thread class module supports the parallel operation of merging search results of different search software or merging search results of the same search software. The computer side of the search library performs dimensionality reduction on the data and displays it using a point graph; The computer side of the search database normalizes the samples and fills in missing values; The computer version of the search library displays the changes before and after quantitative data processing.

8. The automated proteomics mass spectrometer operation and maintenance and data quality control system according to claim 1, characterized in that: The message sender calls the itchat module to mobilize the WeChat interface to send the search result information file and monitoring file; The message sending end calls the email module to send the search result information file and monitoring file.

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