scholarly journals A repository of assays to quantify 10,000 human proteins by SWATH-MS

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
George Rosenberger ◽  
Ching Chiek Koh ◽  
Tiannan Guo ◽  
Hannes L. Röst ◽  
Petri Kouvonen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
A Priori ◽  
Selected Reaction Monitoring ◽  
Spectrometric Method ◽  
Mass Spectrometric Method ◽  
Data Independent Acquisition ◽  
Targeted Analysis ◽  
Human Proteins ◽  
The One ◽  
Multiple Samples

Abstract Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

scholarly journals Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

2018 ◽  
Vol 15 (5) ◽  
pp. 371-378 ◽  
Author(s):  
Ryan Peckner ◽  
Samuel A Myers ◽  
Alvaro Sebastian Vaca Jacome ◽  
Jarrett D Egertson ◽  
Jennifer G Abelin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Targeted Analysis

scholarly journals Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

2020 ◽  
Vol 19 (6) ◽  
pp. 944-959 ◽  
Author(s):  
Tsung-Heng Tsai ◽  
Meena Choi ◽  
Balazs Banfai ◽  
Yansheng Liu ◽  
Brendan X. MacLean ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Profile ◽  
Protein Quantification ◽  
Selected Reaction Monitoring ◽  
Estimation Accuracy ◽  
Spectral Features ◽  
Data Set ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Manual Curation

In bottom-up mass spectrometry-based proteomics, relative protein quantification is often achieved with data-dependent acquisition (DDA), data-independent acquisition (DIA), or selected reaction monitoring (SRM). These workflows quantify proteins by summarizing the abundances of all the spectral features of the protein (e.g. precursor ions, transitions or fragments) in a single value per protein per run. When abundances of some features are inconsistent with the overall protein profile (for technological reasons such as interferences, or for biological reasons such as post-translational modifications), the protein-level summaries and the downstream conclusions are undermined. We propose a statistical approach that automatically detects spectral features with such inconsistent patterns. The detected features can be separately investigated, and if necessary, removed from the data set. We evaluated the proposed approach on a series of benchmark-controlled mixtures and biological investigations with DDA, DIA and SRM data acquisitions. The results demonstrated that it could facilitate and complement manual curation of the data. Moreover, it can improve the estimation accuracy, sensitivity and specificity of detecting differentially abundant proteins, and reproducibility of conclusions across different data processing tools. The approach is implemented as an option in the open-source R-based software MSstats.

Quantitative Confirmation of Dimethoate Residues in Wheat Plants by Single Ion Mass Spectrometry

1979 ◽  
Vol 62 (4) ◽  
pp. 782-785
Author(s):  
Young W Lee ◽  
Neil D Westcott
Keyword(s):  
Mass Spectrometry ◽  
Internal Standard ◽  
Wheat Plant ◽  
Mass Spectrometric ◽  
Spectrometric Method ◽  
Plant Sample ◽  
Minimum Detectable Concentration ◽  
Mass Spectrometric Method ◽  
Base Peak ◽  
Detectable Concentration

Abstract A gas chromatographic-single ion mass spectrometric method was developed for determining dimethoate residues in wheat plants. The base peak (m/e 87) of dimethoate was chosen as the single ion peak, and methyl stearate was used as an internal standard for this analysis. The minimum detectable concentration of dimethoate by this method was about 0.1 ppm for a 20 g wheat plant sample. The recoveries of dimethoate were about 89% at 0.13 ppm and >96% at 0.5-1 ppm.

Confirmation of Phorate, Terbufos, and Their Sulfoxides and Sulfones in Water by Capillary Gas Chromatography /Chemical Ionization Mass Spectrometry

1989 ◽  
Vol 72 (6) ◽  
pp. 987-991
Author(s):  
Steven J Stout ◽  
Adrian R Dacunha ◽  
John E Boyd ◽  
James M Devine
Keyword(s):  
Mass Spectrometry ◽  
Chemical Ionization ◽  
Ionization Mass Spectrometry ◽  
Chemical Ionization Mass Spectrometry ◽  
Spectrometric Method ◽  
Ionization Mass ◽  
Mass Spectrometric Method ◽  
Molecular Weights ◽  
High Carrier ◽  
Positive Ion

Abstract A gas chromatographic/mass spectrometric method capable of confirming phorate, terbufos, their sulfoxides, and sulfones in water is reported. Parents and their metabolites are separated in less than 5 min using a short capillary GC column and high carrier gas linear velocities. Positive ion chemical ionization mass spectrometry generates (M + H) ions indicative of the different molecular weights of the analytes and at least one confirmatory fragment ion for each analyte. Residues have been qualitatively confirmed at the 1 ppb level in fortified water samples from a variety of sources. Apparent residues in control water were less than 0.1 ppb.

scholarly journals Microprobe two-step laser mass spectrometry as an analytical tool for meteoritic samples

1997 ◽  
Vol 178 ◽  
pp. 305-320 ◽  
Author(s):  
Simon J. Clemett ◽  
Richard N. Zare
Keyword(s):  
Mass Spectrometry ◽  
Rapid Heating ◽  
Multiphoton Ionization ◽  
Mass Spectrometric ◽  
Spectrometric Method ◽  
Spectrometric Analysis ◽  
Laser Mass Spectrometry ◽  
Mass Spectrometric Method ◽  
Complex Materials ◽  
Spot Area

Microprobe two-step laser mass spectrometry (μL2MS) is a new mass spectrometric method in which the two essential steps of any mass spectrometric analysis, vaporization and ionization, are carried out using two independent laser sources. In the first step, the output of a pulsed infrared laser is focused on the sample to cause rapid heating in the spot area illuminated, which is typically 40 μm by 40 μm. In the second step, the output of a pulsed ultraviolet laser causes (1+1) resonance-enhanced multiphoton ionization (REMPI) of those desorbed neutral molecules that (1) are able to absorb this UV wavelength and (2) whose ionization potential is less than the energy of two photons of this UV wavelength. The resulting ions are then mass analyzed in a reflectron time-of-flight apparatus. Under suitable conditions fragmentation can be avoided in both the vaporization and ionization steps so that μL2MS can be applied to the analysis of a mixture of molecules. Applications of μL2MS to meteorite samples are presented as a means of detecting trace amounts of certain organic molecules present in complex materials without prior sample preparation, extraction, purification, and separation steps. Moreover, this analysis can be carried out with micrometer spatial resolution so that in favorable cases the presence or absence of certain molecules can be correlated to mineralogical features of the sample.

scholarly journals Specter: linear deconvolution as a new paradigm for targeted analysis of data-independent acquisition mass spectrometry proteomics

2017 ◽  
Author(s):  
Ryan Peckner ◽  
Samuel A Myers ◽  
Jarrett D Egertson ◽  
Richard S Johnson ◽  
Jennifer G. Abelin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Open Source Software ◽  
Software Tool ◽  
Nucleotide Polymorphisms ◽  
Spectral Library ◽  
New Paradigm ◽  
Single Nucleotide ◽  
Data Independent Acquisition ◽  
Targeted Analysis ◽  
Peptide Precursors

AbstractMass spectrometry with data-independent acquisition (DIA) has emerged as a promising method to greatly improve the comprehensiveness and reproducibility of targeted and discovery proteomics, in theory systematically measuring all peptide precursors within a biological sample. Despite the technical maturity of DIA, the analytical challenges involved in discriminating between peptides with similar sequences in convoluted spectra have limited its applicability in important cases, such as the detection of single-nucleotide polymorphisms and alternative site localizations in phosphoproteomics data. We have developed Specter, an open-source software tool that uses linear algebra to deconvolute DIA mixture spectra directly in terms of a spectral library, circumventing the problems associated with typical fragment correlation-based approaches. We validate the sensitivity of Specter and its performance relative to other methods by means of several complex datasets, and show that Specter is able to successfully analyze cases involving highly similar peptides that are typically challenging for DIA analysis methods.

Bioanalysis of therapeutic monoclonal antibody by peptide adsorption-controlled LC–MS

Bioanalysis ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 265-276
Author(s):  
Noritaka Hashii ◽  
Yoshiko Tousaka ◽  
Koji Arai ◽  
Yoshimasa Enoki ◽  
Suguru Fukuda ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Human Serum ◽  
Collaborative Study ◽  
Selected Reaction Monitoring ◽  
Clinical Samples ◽  
Spectrometric Method ◽  
Mass Spectrometric Method ◽  
Therapeutic Monoclonal Antibody ◽  
Study Results ◽  
Peptide Adsorption

Aim: We aimed to develop an easy, low-cost and versatile mass spectrometric method for the bioanalysis of a therapeutic monoclonal antibody (mAb) in human serum that employs peptide adsorption-controlled (PAC)-LC/MS using selected reaction monitoring mode (LC–MS/MS-SRM). Materials & methods: Rituximab was used as a model mAb. To apply the method to human serum samples, a peptide of the complementarity-determining region was selected as the surrogate peptide. The usefulness of PAC-LC–MS/MS-SRM was evaluated by a collaborative study. Results: The calibration curve ranged from 0.5 (or 1.0) to 1000.0 μg/ml. The selectivity, linearity, accuracy and precision met the predefined acceptance criteria. Conclusion: Our method could be a useful bioanalytical method for the quantification of mAbs in clinical samples.

scholarly journals Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion with Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Jason M. Held ◽  
Birgit Schilling ◽  
Alexandria K. D'Souza ◽  
Tara Srinivasan ◽  
Jessica B. Behring ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Posttranslational Modifications ◽  
Development Time ◽  
Assay Development ◽  
Selected Reaction Monitoring ◽  
Label Free ◽  
Data Independent Acquisition ◽  
Key Indicator ◽  
Biomarker Quantitation

The receptor tyrosine kinase ErbB2 is a breast cancer biomarker whose posttranslational modifications (PTMs) are a key indicator of its activation. Quantifying the expression and PTMs of biomarkers such as ErbB2 by selected reaction monitoring (SRM) mass spectrometry has several limitations, including minimal coverage and extensive assay development time. Therefore, we assessed the utility of two high resolution, full scan mass spectrometry approaches, MS1 Filtering and SWATH MS2, for targeted ErbB2 proteomics. Endogenous ErbB2 immunoprecipitated from SK-BR-3 cells was in-gel digested with trypsin, chymotrypsin, Asp-N, or trypsin plus Asp-N in triplicate. Data-dependent acquisition with an AB SCIEX TripleTOF 5600 and MS1 Filtering data processing was used to assess peptide and PTM coverage as well as the reproducibility of enzyme digestion. Data-independent acquisition (SWATH) was also performed for MS2 quantitation. MS1 Filtering and SWATH MS2 allow quantitation of all detected analytes after acquisition, enabling the use of multiple proteases for quantitative assessment of target proteins. Combining high resolution proteomics with multiprotease digestion enabled quantitative mapping of ErbB2 with excellent reproducibility, improved amino acid sequence and PTM coverage, and decreased assay development time compared to typical SRM assays. These results demonstrate that high resolution quantitative proteomic approaches are an effective tool for targeted biomarker quantitation.

scholarly journals Liquid Chromatography–Tandem Mass Spectrometry for Detection of Low Concentrations of 21 Benzodiazepines, Metabolites, and Analogs in Urine: Method with Forensic Applications

2006 ◽  
Vol 52 (7) ◽  
pp. 1346-1355 ◽  
Author(s):  
Oscar Quintela ◽  
François-Ludovic Sauvage ◽  
Fabienne Charvier ◽  
Jean-Michel Gaulier ◽  
Gérard Lachâtre ◽  
...  
Keyword(s):  
Sexual Assault ◽  
Chromatographic Separation ◽  
Solid Phase ◽  
Reversed Phase ◽  
Selected Reaction Monitoring ◽  
Spectrometric Method ◽  
Tandem Mass ◽  
Mass Spectrometric Method ◽  
Low Concentrations ◽  
Tandem Mass Spectrometric

Abstract Background: Commonly used methods for detecting benzodiazepines (BZPs) and BZP-like substances, such as zolpidem and zopiclone, may not detect low concentrations of these drugs. We developed a liquid chromatographic–tandem mass spectrometric method for identifying these drugs and their relevant metabolites. Methods: We extracted BZPs from urine by solid-phase extraction with a mixed-mode phase (OASIS® HLB cartridges). Chromatographic separation was performed with a Waters XTerra MS C18 [150 × 2.1 mm (i.d.); bead size, 5 μm] reversed-phase column with deuterated analogs of the analytes as internal standards (IS). Detection was performed with a triple-quadruple mass spectrometer that monitored 2 specific transitions per compound in the electrospray, positive-ion selected-reaction monitoring mode. We tested this technique on urine samples from 12 healthy volunteers and 1 forensic sample obtained in a case of alleged drug-facilitated sexual assault. Results: Chromatographic separation was achieved within 18 min. The linear dynamic ranges extended from 0.02 or 0.1 μg/L (depending on the drug or metabolite) to 50 μg/L. Extraction recovery (range) was 77%–110%. Limits of detection were ≤0.05 μg/L. No ion suppression was seen except for alprazolam, for which baseline decreased by almost 20%. In the forensic urine sample, the method detected alprazolam (3.5 μg/L) and its characteristic metabolite, α-hydroxyalprazolam (0.17 μg/L). Conclusion: This method measured low concentrations of BZPs and BZP-like substances and might be useful for analyses of urine in suspected drug-facilitated sexual assault cases.

Sign in / Sign up

Export Citation Format

Share Document