Severity: Warning
Message: file_get_contents(https://...@pubfacts.com&api_key=b8daa3ad693db53b1410957c26c9a51b4908&a=1): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests
Filename: helpers/my_audit_helper.php
Line Number: 176
Backtrace:
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 176
Function: file_get_contents
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 250
Function: simplexml_load_file_from_url
File: /var/www/html/application/helpers/my_audit_helper.php
Line: 3122
Function: getPubMedXML
File: /var/www/html/application/controllers/Detail.php
Line: 575
Function: pubMedSearch_Global
File: /var/www/html/application/controllers/Detail.php
Line: 489
Function: pubMedGetRelatedKeyword
File: /var/www/html/index.php
Line: 316
Function: require_once
Activity-based protein profiling (ABPP) is a powerful chemical proteomic method for studying protein activity, modifications, and interactions in a high-throughput manner. In ABPP experiments, accurate quantification is crucial to determine the extent of probe labeling at the level of either target proteins or specific amino acid side chains. CIMAGE has been developed as an in-house quantification software specifically designed for ABPP data analysis that incorporates (1) a relaxed peak extraction algorithm and (2) stringent post-quantification checks for efficient and accurate quantification. It also can generate table and image data for users to conveniently visualize their results. Here we provide a retrospective introduction of the software and describe our recent upgrade efforts to enable (1) interfacing with different database search engines as input, (2) triplex quantification of ABPP data by reductive dimethylation, and (3) envelope checking for chemical elements with special isotopic distributions. We show that the updated CIMAGE can maintain its ability to quantify ABPP data with dramatic depth and high accuracy, and it also has similar quantification performance in benchmarked SILAC data as compared with MaxQuant. We believe that CIMAGE2.0 will continue to serve as a powerful analytical tool for ABPP studies.
Download full-text PDF |
Source |
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http://dx.doi.org/10.1021/acs.jproteome.1c00455 | DOI Listing |
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