How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data

High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis. pFind 3 features a swift open search workflow that is adept at unco...

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Autores principales: Shao, Guangcan, Cao, Yong, Chen, Zhenlin, Liu, Chao, Li, Shangtong, Chi, Hao, Dong, Meng-Qiu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biophysics Reports Editorial Office 2021
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244800/
https://www.ncbi.nlm.nih.gov/pubmed/37287487
http://dx.doi.org/10.52601/bpr.2021.210004
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author Shao, Guangcan
Cao, Yong
Chen, Zhenlin
Liu, Chao
Li, Shangtong
Chi, Hao
Dong, Meng-Qiu
author_facet Shao, Guangcan
Cao, Yong
Chen, Zhenlin
Liu, Chao
Li, Shangtong
Chi, Hao
Dong, Meng-Qiu
author_sort Shao, Guangcan
collection PubMed
description High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis. pFind 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using pFind 3 in conjunction with pParse for data pre-processing and if needed, pQuant for quantitation. This streamlined pParse-pFind-pQuant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on (15)N-labeling, SILAC-labeling, or TMT/iTRAQ labeling.
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spelling pubmed-102448002023-06-07 How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data Shao, Guangcan Cao, Yong Chen, Zhenlin Liu, Chao Li, Shangtong Chi, Hao Dong, Meng-Qiu Biophys Rep Protocol High-throughput proteomics based on mass spectrometry (MS) analysis has permeated biomedical science and propelled numerous research projects. pFind 3 is a database search engine for high-speed and in-depth proteomics data analysis. pFind 3 features a swift open search workflow that is adept at uncovering less obvious information such as unexpected modifications or mutations that would have gone unnoticed using a conventional data analysis pipeline. In this protocol, we provide step-by-step instructions to help users mastering various types of data analysis using pFind 3 in conjunction with pParse for data pre-processing and if needed, pQuant for quantitation. This streamlined pParse-pFind-pQuant workflow offers exceptional sensitivity, precision, and speed. It can be easily implemented in any laboratory in need of identifying peptides, proteins, or post-translational modifications, or of quantitation based on (15)N-labeling, SILAC-labeling, or TMT/iTRAQ labeling. Biophysics Reports Editorial Office 2021-06-30 /pmc/articles/PMC10244800/ /pubmed/37287487 http://dx.doi.org/10.52601/bpr.2021.210004 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Protocol
Shao, Guangcan
Cao, Yong
Chen, Zhenlin
Liu, Chao
Li, Shangtong
Chi, Hao
Dong, Meng-Qiu
How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title_full How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title_fullStr How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title_full_unstemmed How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title_short How to use open-pFind in deep proteomics data analysis?— A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
title_sort how to use open-pfind in deep proteomics data analysis?— a protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10244800/
https://www.ncbi.nlm.nih.gov/pubmed/37287487
http://dx.doi.org/10.52601/bpr.2021.210004
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