scholarly journals Comprehensive peptide quantification for data independent acquisition mass spectrometry using chromatogram libraries

2018 ◽  
Author(s):  
Brian C. Searle ◽  
Lindsay K. Pino ◽  
Jarrett D. Egertson ◽  
Ying S. Ting ◽  
Robert T. Lawrence ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Retention Time ◽  
Software Tool ◽  
Yeast Cells ◽  
Chromatographic Peak ◽  
Peak Shape ◽  
Specific Mass ◽  
Protein Databases ◽  
Data Independent Acquisition ◽  
Peptide Detection

ABSTRACTData independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. We introduce a new experimental workflow that uses this technique to construct chromatogram libraries that capture fragment ion chromatographic peak shape and retention time for every detectable peptide in an experiment. These coordinates calibrate information in spectrum libraries or protein databases to a specific mass spectrometer and chromatography setup, and enable sensitive peptide detection in quantitative experiments. We also present EncyclopeDIA, a software tool for generating and searching chromatogram libraries, and demonstrate the performance of our workflow by quantifying proteins in human and yeast cells. We find that by exploiting calibrated retention time and fragmentation specificity in chromatogram libraries, EncyclopeDIA can detect and quantify >50% more peptides from DIA experiments than with DDA-based spectrum libraries alone.

scholarly journals Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Brian C. Searle ◽  
Lindsay K. Pino ◽  
Jarrett D. Egertson ◽  
Ying S. Ting ◽  
Robert T. Lawrence ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Independent Acquisition ◽  
Peptide Detection ◽  
Detection And Quantification

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.

scholarly journals PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

2017 ◽  
Vol 14 (9) ◽  
pp. 903-908 ◽  
Author(s):  
Ying S Ting ◽  
Jarrett D Egertson ◽  
James G Bollinger ◽  
Brian C Searle ◽  
Samuel H Payne ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Tandem Mass ◽  
Free Peptide ◽  
Data Independent Acquisition ◽  
Peptide Detection ◽  
Tandem Mass Spectrometry Data

scholarly journals Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry

2015 ◽  
Vol 14 (10) ◽  
pp. 2800-2813 ◽  
Author(s):  
Sarah J. Parker ◽  
Hannes Rost ◽  
George Rosenberger ◽  
Ben C. Collins ◽  
Lars Malmström ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Retention Time ◽  
Data Independent Acquisition ◽  
Time Standards

scholarly journals A flexible workflow for building spectral libraries from narrow window data independent acquisition mass spectrometry data

2021 ◽  
Author(s):  
Lilian R. Heil ◽  
William E. Fondrie ◽  
Christopher D. McGann ◽  
Alexander J. Federation ◽  
William S. Noble ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Spectral Library ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Peptide Detection ◽  
Phosphorylated Peptides ◽  
Single Mass ◽  
Fragmentation Patterns ◽  
Spectral Libraries

Advances in library-based methods for peptide detection from data independent acquisition (DIA) mass spectrometry have made it possible to detect and quantify tens of thousands of peptides in a single mass spectrometry run. However, many of these methods rely on a comprehensive, high quality spectral library containing information about the expected retention time and fragmentation patterns of peptides in the sample. Empirical spectral libraries are often generated through data-dependent acquisition and may suffer from biases as a result. Spectral libraries can be generated in silico but these models are not trained to handle all possible post-translational modifications. Here, we propose a false discovery rate controlled spectrum-centric search workflow to generate spectral libraries directly from gas-phase fractionated DIA tandem mass spectrometry data. We demonstrate that this strategy is able to detect phosphorylated peptides and can be used to generate a spectral library for accurate peptide detection and quantitation in wide window DIA data. We compare the results of this search workflow to other library-free approaches and demonstrate that our search is competitive in terms of accuracy and sensitivity. These results demonstrate that the proposed workflow has the capacity to generate spectral libraries while avoiding the limitations of other methods.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

Studies on Chromatographic Fractioning by Cations Exchangers of a Bovine Hemoglobin Hydrolysate

2018 ◽  
Vol 69 (10) ◽  
pp. 2794-2798
Author(s):  
Alina Diana Panainte ◽  
Ionela Daniela Morariu ◽  
Nela Bibire ◽  
Madalina Vieriu ◽  
Gladiola Tantaru ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Retention Time ◽  
Chromatographic Separation ◽  
Bovine Hemoglobin ◽  
Reverse Phase ◽  
Hplc System ◽  
Fast Flow ◽  
Hydrolysis Of ◽  
Phase Column

A peptidic hydrolysate has been obtained through hydrolysis of bovine hemoglobin using pepsin. The fractioning of the hydrolysate was performed on a column packed with CM-Sepharose Fast Flow. The hydrolysate and each fraction was filtered and then injected into a HPLC system equipped with a Vydak C4 reverse phase column (0.46 x 25 cm), suitable for the chromatographic separation of large peptides with 20 to 30 amino acids. The detection was done using mass spectrometry, and the retention time, size and distribution of the peptides were determined.

Sign in / Sign up

Export Citation Format

Share Document