Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert

French, William R.; Zimmerman, Lisa J.; Schilling, Birgit; Gibson, Bradford W.; Miller, Christine; Townsend, R. Reid; Sherrod, Stacy D.; Goodwin, Cody R.; McLean, John A.; Tabb, David L.

doi:10.1021/pr500886y

Cited by 41 publications

(28 citation statements)

References 28 publications

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“…Further, peptide identification, filtering, and protein assembly were done with the IDPicker 3.1 algorithm with a maximum Q value of 2% for PSM. 66 Resulting PSMs were manually inspected, and MS 2 spectra were examined to confirm correct assignment of PTMs. In addition, known peptides containing 3-HyP were searched for manually by searching possible ion masses in the raw data using Thermo Xcalibur software.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

et al. 2015

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Collagen IV is the main structural protein that provides a scaffold for assembly of basement membrane proteins. Posttranslational modifications such as hydroxylation of proline and lysine and glycosylation of lysine are essential for the functioning of collagen IV triple-helical molecules. These modifications are highly abundant posing a difficult challenge for in-depth characterization of collagen IV using conventional proteomics approaches. Herein, we implemented an integrated pipeline combining high-resolution mass spectrometry with different fragmentation techniques and an optimized bioinformatics workflow to study posttranslational modifications in mouse collagen IV. We achieved 82% sequence coverage for the α1 chain, mapping 39 glycosylated hydroxylysine, 148 4-hydroxyproline, and seven 3-hydroxyproline residues. Further, we employed our pipeline to map the modifications on human collagen IV and achieved 85% sequence coverage for the α1 chain, mapping 35 glycosylated hydroxylysine, 163 4-hydroxyproline, and 14 3-hydroxyproline residues. Although lysine glycosylation heterogeneity was observed in both mouse and human, 21 conserved sites were identified. Likewise, five 3-hydroxyproline residues were conserved between mouse and human, suggesting that these modification sites are important for collagen IV function. Collectively, these are the first comprehensive maps of hydroxylation and glycosylation sites in collagen IV, which lay the foundation for dissecting the key role of these modifications in health and disease.

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Section: Methodsmentioning

confidence: 99%

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

et al. 2015

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“…The filter settings conducted vendor library peak picking on all types of scans within the files ("peakPicking true 1-"). For Waters instruments, the same software was used, but the CantWaiT filter in ProteoWizard was used for peak picking ("peakPicking cwt msLevel ϭ 2-") and the TurboCharger filter provided precursor charges (15). Using "ProteinPilot" peak picking, AB SCIEX .wiff files were first processed through the AB SCIEX MS Converter to produce mzML files.…”

Section: Methodsmentioning

confidence: 99%

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses*

Bennett

Xia

Bystrom³

et al. 2015

Molecular & Cellular Proteomics

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Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to, such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114. Molecular & Cellular Proteomics 14: 10.1074/mcp.O115.051888, 3299-3309, 2015.The broad-reaching use and application of mass spectrometry-based proteomics in the international research commu-

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“…155,156 The quality and validation of peak detection from increasingly complex datasets remains an area of intense research efforts. 157,158 …”

Section: Preparation Of High Content Mass Spectral Data For Metabolmentioning

confidence: 99%

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

2017

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The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accellerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

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Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert

Cited by 41 publications

References 28 publications

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses*

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites

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