In-depth evaluation of software tools for data-independent acquisition based label-free quantification

PROTEOMICS ◽  
2015 ◽  
Vol 15 (18) ◽  
pp. 3140-3151 ◽  
Author(s):  
Jörg Kuharev ◽  
Pedro Navarro ◽  
Ute Distler ◽  
Olaf Jahn ◽  
Stefan Tenzer
Keyword(s):  
Software Tools ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

Label-Free Quantification by Data Independent Acquisition Mass Spectrometry to Map Cardiovascular Proteomes

2016 ◽  
pp. 227-245
Author(s):  
Sarah J. Parker ◽  
Ronald J. Holewinski ◽  
Irina Tchernyshyov ◽  
Vidya Venkatraman ◽  
Laurie Parker ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

Label-free quantification in ion mobility–enhanced data-independent acquisition proteomics

2016 ◽  
Vol 11 (4) ◽  
pp. 795-812 ◽  
Author(s):  
Ute Distler ◽  
Jörg Kuharev ◽  
Pedro Navarro ◽  
Stefan Tenzer
Keyword(s):  
Ion Mobility ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Free Quantification

scholarly journals Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC–MS/MS

2015 ◽  
Vol 14 (11) ◽  
pp. 4581-4593 ◽  
Author(s):  
Aivett Bilbao ◽  
Ying Zhang ◽  
Emmanuel Varesio ◽  
Jeremy Luban ◽  
Caterina Strambio-De-Castillia ◽  
...  
Keyword(s):  
Outlier Detection ◽  
Label Free ◽  
Label Free Quantification ◽  
Data Independent Acquisition ◽  
Fragment Ions ◽  
Free Quantification

scholarly journals Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

Proteomes ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 15
Author(s):  
Subina Mehta ◽  
Caleb W. Easterly ◽  
Ray Sajulga ◽  
Robert J. Millikin ◽  
Andrea Argentini ◽  
...  
Keyword(s):  
Dynamic Range ◽  
Software Tools ◽  
Protein Quantification ◽  
Label Free ◽  
Post Translational Modifications ◽  
Label Free Quantification ◽  
File Formats ◽  
Rigorous Testing ◽  
The Galaxy ◽  
Free Quantification

For mass spectrometry-based peptide and protein quantification, label-free quantification (LFQ) based on precursor mass peak (MS1) intensities is considered reliable due to its dynamic range, reproducibility, and accuracy. LFQ enables peptide-level quantitation, which is useful in proteomics (analyzing peptides carrying post-translational modifications) and multi-omics studies such as metaproteomics (analyzing taxon-specific microbial peptides) and proteogenomics (analyzing non-canonical sequences). Bioinformatics workflows accessible via the Galaxy platform have proven useful for analysis of such complex multi-omic studies. However, workflows within the Galaxy platform have lacked well-tested LFQ tools. In this study, we have evaluated moFF and FlashLFQ, two open-source LFQ tools, and implemented them within the Galaxy platform to offer access and use via established workflows. Through rigorous testing and communication with the tool developers, we have optimized the performance of each tool. Software features evaluated include: (a) match-between-runs (MBR); (b) using multiple file-formats as input for improved quantification; (c) use of containers and/or conda packages; (d) parameters needed for analyzing large datasets; and (e) optimization and validation of software performance. This work establishes a process for software implementation, optimization, and validation, and offers access to two robust software tools for LFQ-based analysis within the Galaxy platform.

scholarly journals Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins

2019 ◽  
Vol 18 (4) ◽  
pp. 1477-1485 ◽  
Author(s):  
Johannes Griss ◽  
Florian Stanek ◽  
Otto Hudecz ◽  
Gerhard Dürnberger ◽  
Yasset Perez-Riverol ◽  
...  
Keyword(s):  
Spectral Clustering ◽  
Label Free ◽  
Label Free Quantification ◽  
Free Quantification

Global Analysis of Protein Expression in A549 Cells After Prolonged Nicotine Exposure by Using Label-free Quantification

2021 ◽  
Vol 41 (8) ◽  
pp. 3833-3842
Author(s):  
SASIKARN KOMKLEOW ◽  
CHURAT WEERAPHAN ◽  
DARANEE CHOKCHAICHAMNANKIT ◽  
PAPADA CHAISURIYA ◽  
CHRIS VERATHAMJAMRAS ◽  
...  
Keyword(s):  
Protein Expression ◽  
Global Analysis ◽  
A549 Cells ◽  
Nicotine Exposure ◽  
Label Free ◽  
Label Free Quantification ◽  
Free Quantification

Label-Free Quantification of Anticancer Drug Imatinib in Human Plasma with Surface Enhanced Raman Spectroscopy

2018 ◽  
Vol 90 (21) ◽  
pp. 12670-12677 ◽  
Author(s):  
Stefano Fornasaro ◽  
Alois Bonifacio ◽  
Elena Marangon ◽  
Mauro Buzzo ◽  
Giuseppe Toffoli ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Human Plasma ◽  
Anticancer Drug ◽  
Surface Enhanced Raman Spectroscopy ◽  
Label Free ◽  
Label Free Quantification ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Free Quantification
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