scholarly journals PulseDIA: in-depth data independent acquisition mass spectrometry using enhanced gas phase fractionation

2019 ◽  
Author(s):  
Xue Cai ◽  
Weigang Ge ◽  
Xiao Yi ◽  
Rui Sun ◽  
Jiang Zhu ◽  
...  
Keyword(s):  
Gas Phase ◽  
Mass Range ◽  
Tissue Samples ◽  
Mass Spectrometers ◽  
Data Independent Acquisition ◽  
Window Width ◽  
Specificity And Sensitivity ◽  
Peptide Precursors ◽  
Gas Phase Separation ◽  
Higher Sensitivity

ABSTRACTAn inherent bottleneck of data independent acquisition (DIA) analysis by Orbitrap-based mass spectrometers is the relatively large window width due to the relatively slow scanning rate compared to TOF. Here we present a novel gas phase separation and MS acquisition method called PulseDIA-MS, which improves the specificity and sensitivity of Orbitrap-based DIA analysis. This is achieved by dividing the ordinary DIA-MS analysis covering the entire mass range into multiple injections for DIA-MS analyses with complementary windows. Using standard HeLa digests, the PulseDIA method identified 69,530 peptide precursors from 9,337 protein groups with ten MS injections of 30 min LC gradient. The PulseDIA scheme containing two complementary windows led to the highest gain of peptide and protein identifications per time unit compared to the conventional 30 min DIA method. We further applied the method to profile the proteome of 18 cholangiocarcinoma (CCA) tissue samples (benign and malignant) from nine patients. PulseDIA identified 7,796 protein groups in these CCA samples, with 14% increase of protein identifications, compared to the conventional DIA method. The missing value for protein matrix dropped by 7% with PulseDIA acquisition. 681 proteins were significantly dysregulated in tumorous CCA samples. Together, we presented and benchmarked an alternative DIA method with higher sensitivity and lower missing rate.

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.

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 The SAMI Galaxy Survey: reconciling strong emission line metallicity diagnostics using metallicity gradients

2021 ◽  
Vol 502 (3) ◽  
pp. 3357-3373
Author(s):  
Henry Poetrodjojo ◽  
Brent Groves ◽  
Lisa J Kewley ◽  
Sarah M Sweet ◽  
Sebastian F Sanchez ◽  
...  
Keyword(s):  
Emission Line ◽  
Electron Temperature ◽  
Gas Phase ◽  
Mass Range ◽  
Accurate Method ◽  
Emission Lines ◽  
Mass Relation ◽  
Strong Emission ◽  
Data Release ◽  
Accurate Comparison

ABSTRACT We measure the gas-phase metallicity gradients of 248 galaxies selected from Data Release 2 of the SAMI Galaxy Survey. We demonstrate that there are large systematic discrepancies between the metallicity gradients derived using common strong emission line metallicity diagnostics. We determine which pairs of diagnostics have Spearman’s rank coefficients greater than 0.6 and provide linear conversions to allow the accurate comparison of metallicity gradients derived using different strong emission line diagnostics. For galaxies within the mass range 8.5 < log (M/M⊙) < 11.0, we find discrepancies of up to 0.11 dex/Re between seven popular diagnostics in the metallicity gradient–mass relation. We find a suggestion of a break in the metallicity gradient–mass relation, where the slope shifts from negative to positive, occurs between 9.5 < log (M/M⊙) < 10.5 for the seven chosen diagnostics. Applying our conversions to the metallicity gradient–mass relation, we reduce the maximum dispersion from 0.11 dex/Re to 0.02 dex/Re. These conversions provide the most accurate method of converting metallicity gradients when key emission lines are unavailable. We find that diagnostics that share common sets of emission line ratios agree best, and that diagnostics calibrated through the electron temperature provide more consistent results compared to those calibrated through photoionization models.

scholarly journals Data-Independent Acquisition for the Quantification and Identification of Metabolites in Plasma

Metabolites ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 514
Author(s):  
Tom van der Laan ◽  
Isabelle Boom ◽  
Joshua Maliepaard ◽  
Anne-Charlotte Dubbelman ◽  
Amy C. Harms ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Mass Range ◽  
Correct Identification ◽  
Hydrophilic Interaction ◽  
Specific Mass ◽  
Structural Isomers ◽  
Data Independent Acquisition ◽  
Targeted Analysis ◽  
Theoretical Mass ◽  
Accurate Quantification

A popular fragmentation technique for non-targeted analysis is called data-independent acquisition (DIA), because it provides fragmentation data for all analytes in a specific mass range. In this work, we demonstrated the strengths and weaknesses of DIA. Two types of chromatography (fractionation/3 min and hydrophilic interaction liquid chromatography (HILIC)/18 min) and three DIA protocols (variable sequential window acquisition of all theoretical mass spectra (SWATH), fixed SWATH and MSALL) were used to evaluate the performance of DIA. Our results show that fast chromatography and MSALL often results in product ion overlap and complex MS/MS spectra, which reduces the quantitative and qualitative power of these DIA protocols. The combination of SWATH and HILIC allowed for the correct identification of 20 metabolites using the NIST library. After SWATH window customization (i.e., variable SWATH), we were able to quantify ten structural isomers with a mean accuracy of 103% (91–113%). The robustness of the variable SWATH and HILIC method was demonstrated by the accurate quantification of these structural isomers in 10 highly diverse blood samples. Since the combination of variable SWATH and HILIC results in good quantitative and qualitative fragmentation data, it is promising for both targeted and untargeted platforms. This should decrease the number of platforms needed in metabolomics and increase the value of a single analysis.

Hydrogen Production via the Iron/Iron Oxide Looping Cycle

2011 ◽  
Author(s):  
A. Singh ◽  
F. Al-Raqom ◽  
J. Klausner ◽  
J. Petrasch
Keyword(s):  
Iron Oxide ◽  
Hydrogen Production ◽  
Gas Phase ◽  
Energy Content ◽  
Operation Conditions ◽  
Iron Oxide Reduction ◽  
Temperature Ranges ◽  
Iron Iron ◽  
Gas Phase Separation ◽  
Distinct Temperature

The iron/iron-oxide looping cycle has the potential to produce high purity hydrogen from coal or natural gas without the need for gas phase separation: Hydrogen is produced from steam oxidation of iron or Wustite yielding primarily Magnetite; Magnetite is then reduced back to iron/Wustite using syngas (CO+H2). A system model has been developed to identify favorable operation conditions and process configurations. Process configurations for three distinct temperature ranges, (i) 500–950 K, (ii) 950–1100 K, and (iii) 1100–1200 K have been developed. The energy content of high temperature syngas from conventional coal gasifiers is sufficient to drive the looping process throughout the temperature range considered. Temperatures around 1000 K are advantageous for both the hydrogen production step and the iron oxide reduction step. Simulations of a large number of subsequent cycles indicate that quasi-steady operation is reached after approximately 5 cycles. Comparison of simulations and experiments indicate that the process is currently limited by chemical kinetics at lower temperatures. Therefore, product recirculation should be used for a scaled-up process to increase reactant residence times while maintaining sufficient fluidization velocity.

scholarly journals MALDI TIMS IMS of Disialoganglioside Isomers – GD1a and GD1b in Murine Brain Tissue

2021 ◽  
Author(s):  
Katerina Djambazova ◽  
Martin Dufresne ◽  
Lukasz Migas ◽  
Angela Kruse ◽  
Raf Van de Plas ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Phase Separation ◽  
Sialic Acid ◽  
Gas Phase ◽  
Sialic Acid Residue ◽  
Spinal Cord Tissue ◽  
Total Ganglioside ◽  
Tissue Sections ◽  
Maldi Ims ◽  
Gas Phase Separation

Gangliosides are classified as acidic glycosphingolipids, containing ceramide moieties and oligosaccharide chains with one or multiple sialic acid residue(s). The presence of multiple sialylation sites gives rise to highly diverse isomeric structures with distinct biological roles. Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) enables the untargeted spatial analysis of gangliosides, among other biomolecules, directly from tissue sections. Integrating trapped ion mobility mass spectrometry (TIMS), a gas-phase separation technology, with MALDI IMS allows for the investi-gation of isomeric lipid structures in situ. Here we demonstrate the gas-phase separation of disialoganglioside isomers GD1a and GD1b that differ in the position of a sialic acid residue, in a standard mixture of both isomers, a total ganglioside extract, and directly from thin tissue sections. The unique spatial distributions of GD1a/b (d36:1) and GD1a/b (d38:1) were deter-mined from rat hippocampus, as well as in a spinal cord tissue section.

scholarly journals Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

2019 ◽  
Author(s):  
Rui Sun ◽  
Christie Hunter ◽  
Chen Chen ◽  
Weigang Ge ◽  
Nick Morrice ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Biomarker Discovery ◽  
Single Shot ◽  
Protein Biomarkers ◽  
Differential Abundance ◽  
Tissue Samples ◽  
Peptide Precursors ◽  
High Consistency ◽  
Method R ◽  
Acquisition Method

ABSTRACTWe report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 15-min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration and OpenSWATH software for data analysis.We applied the method to a cohort 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).Overall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.

scholarly journals Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user's perspective

2021 ◽  
Author(s):  
Alejandro Fernandez-Vega ◽  
Federica Farabegoli ◽  
Maria Mercedes Alonso-Martinez ◽  
Ignacio Ortea
Keyword(s):  
Data Analysis ◽  
Quantitative Proteomics ◽  
Real Life ◽  
Analysis Tool ◽  
Proteomics Data ◽  
Mass Spectrometers ◽  
Data Independent Acquisition ◽  
Proteomics Experiment ◽  
Under Sampling ◽  
The One

Data-independent acquisition (DIA) methods have gained great popularity in bottom-up quantitative proteomics, as they overcome the irreproducibility and under-sampling limitations of data-dependent acquisition (DDA). diaPASEF, recently developed for the timsTOF Pro mass spectrometers, has brought improvements to DIA, providing additional ion separation (in the ion mobility dimension) and increasing sensitivity. Several studies have benchmarked different workflows for DIA quantitative proteomics, but mostly using instruments from Sciex and Thermo, and therefore, the results are not extrapolable to diaPASEF data. In this work, using a real-life sample set like the one that can be found in any proteomics experiment, we compared the results of analyzing PASEF data with different combinations of library-based and library-free analysis, combining the tools of the FragPipe suite, DIA-NN and including MS1-level LFQ with DDA-PASEF data, and also comparing with the workflows possible in Spectronaut. We verified that library-independent workflows, not so efficient not so long ago, have greatly improved in the recent versions of the software tools, and now perform as well or even better than library-based ones. We report here information so that the user who is going to conduct a relative quantitative proteomics study using a timsTOF Pro mass spectrometer can make an informed decision on how to acquire (diaPASEF for DIA analysis, or DDA-PASEF for MS1-level LFQ) the samples, and what can be expected depending on the data analysis tool used, among the different alternatives offered by the recently optimized tools for TIMS-PASEF data analysis.

scholarly journals DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Mukul K. Midha ◽  
David S. Campbell ◽  
Charu Kapil ◽  
Ulrike Kusebauch ◽  
Michael R. Hoopmann ◽  
...  
Keyword(s):  
Quality Control ◽  
Assessment Tool ◽  
Software Tool ◽  
Mass Range ◽  
Systematic Evaluation ◽  
Label Free ◽  
Mass Spectral ◽  
Data Independent Acquisition ◽  
Theoretical Mass ◽  
Spectral Libraries

Abstract Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity.

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