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

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

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 A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

2019 ◽  
Author(s):  
Dorte B. Bekker-Jensen ◽  
Ana Martínez del Val ◽  
Sophia Steigerwald ◽  
Patrick Rüther ◽  
Kyle Fort ◽  
...  
Keyword(s):  
Mass Spectrometer ◽  
Ion Mobility ◽  
Rat Tissues ◽  
Label Free ◽  
Mass Spectrometers ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
Orbitrap Mass Spectrometer ◽  
Peptide Precursors ◽  
Free Quantification

ABSTRACTState-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 unique peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 minute LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

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

scholarly journals A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

2020 ◽  
Vol 19 (4) ◽  
pp. 716-729 ◽  
Author(s):  
Dorte B. Bekker-Jensen ◽  
Ana Martínez-Val ◽  
Sophia Steigerwald ◽  
Patrick Rüther ◽  
Kyle L. Fort ◽  
...  
Keyword(s):  
Mass Spectrometer ◽  
Ion Mobility ◽  
Rat Tissues ◽  
Label Free ◽  
Mass Spectrometers ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
Orbitrap Mass Spectrometer ◽  
Peptide Precursors ◽  
Free Quantification

State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

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
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