Building high-quality assay libraries for targeted analysis of SWATH MS data

Schubert, Olga T.; Gillet, Ludovic; Collins, Ben C.; Navarro, Pedro J.; Rosenberger, George; Wolski, Witold; Lam, Henry H N; Amodei, Dario; Mallick, Parag; MacLean, Brendan; Aebersold, Ruedi

doi:10.1038/nprot.2015.015

Cited by 307 publications

(334 citation statements)

References 60 publications

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“…However, it is important to quantify CML-and CELmodified albumin, as these modifications constitute the predominant AGEs. Several mass-spectrometry-based targeted quantification approaches, including multiple reaction monitoring, parallel reaction monitoring, and SWATH, have become powerful tools and rely heavily on fragment ion library (39,40). In this context, we constructed a fragment ion library for the synthetically AML-, CML-, and CEL-modified peptides of albumin by using high-resolution accurate mass spectrometer followed by rigorous inspection and validation of MS/MS spectra.…”

Section: Discussionmentioning

confidence: 99%

Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE

Korwar

Vannuruswamy

Jagadeeshaprasad

et al. 2015

Molecular & Cellular Proteomics

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Human serum albumin is one of the most abundant plasma proteins that readily undergoes glycation, thus glycated albumin has been suggested as an additional marker for monitoring glycemic status. Hitherto, only Amadori-modified peptides of albumin were quantified. In this study, we report the construction of fragment ion library for Amadori-modified lysine (AML), N()-(carboxymethyl)lysine (CML)-, and N()-(carboxyethyl)lysine (CEL)-modified peptides of the corresponding synthetically modified albumin using high resolution accurate mass spectrometry (HR/AM). The glycated peptides were manually inspected and validated for their modification. Further, the fragment ion library was used for quantification of glycated peptides of albumin in the context of diabetes. Targeted Sequential Window Acquisition of all THeoretical Mass Spectra (SWATH) analysis in pooled plasma samples of control, prediabetes, diabetes, and microalbuminuria, has led to identification and quantification of 13 glycated peptides comprised of four AML, seven CML, and two CEL modifications, representing nine lysine sites of albumin. Five lysine sites namely K549, K438, K490, K88, and K375, were observed to be highly sensitive for glycation modification as their respective m/z showed maximum fold change and had both AML and CML modifications. Thus, peptides involving these lysine sites could be potential novel markers to assess the degree of glycation in diabetes. Molecular & Cellular Proteomics

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Section: Discussionmentioning

confidence: 99%

Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE

Korwar

Vannuruswamy

Jagadeeshaprasad

et al. 2015

Molecular & Cellular Proteomics

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“…To extract quantitative information from such digital SWATH-MS data, high-quality assay libraries are required (109,111). Such libraries contain retention-time and fragmentation information of the peptides to be quantified.…”

Section: Identification and Quantification Of Mhc-associated Peptidesmentioning

confidence: 99%

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

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197

118

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The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. Molecular & Cellular

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“…Recent advances in proteomics make it possible to quantify many proteins in large numbers of samples in model organisms with small genomes (Picotti et al, 2013;Schubert et al, 2015). However, these technologies are not yet applicable to plants.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis

et al. 2017

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ORCID IDs: 0000-0001-6809-0266 (C.M.F.); 0000-0001-8593-1741 (M.G.A.); 0000-0002-6113-9570 (R.S.); 0000-0002-4900-1763 (M.S.); 0000-0001-8918-0711 (J.J.B.K.)Central metabolism is a coordinated network that is regulated at multiple levels by resource availability and by environmental and developmental cues. Its genetic architecture has been investigated by mapping metabolite quantitative trait loci (QTL). A more direct approach is to identify enzyme activity QTL, which distinguishes between cis-QTL in structural genes encoding enzymes and regulatory trans-QTL. Using genome-wide association studies, we mapped QTL for 24 enzyme activities, nine metabolites, three structural components, and biomass in Arabidopsis thaliana. We detected strong cis-QTL for five enzyme activities. A cis-QTL for UDP-glucose pyrophosphorylase activity in the UGP1 promoter is maintained through balancing selection. Variation in acid invertase activity reflects multiple evolutionary events in the promoter and coding region of VAC-INV. cis-QTL were also detected for ADP-glucose pyrophosphorylase, fumarase, and phosphoglucose isomerase activity. We detected many trans-QTL, including transcription factors, E3 ligases, protein targeting components, and protein kinases, and validated some by knockout analysis. trans-QTL are more frequent but tend to have smaller individual effects than cis-QTL. We detected many colocalized QTL, including a multitrait QTL on chromosome 4 that affects six enzyme activities, three metabolites, protein, and biomass. These traits are coordinately modified by different ACCELERATED CELL DEATH6 alleles, revealing a trade-off between metabolism and defense against biotic stress.

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Building high-quality assay libraries for targeted analysis of SWATH MS data

Cited by 307 publications

References 60 publications

Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE

Development of Diagnostic Fragment Ion Library for Glycated Peptides of Human Serum Albumin: Targeted Quantification in Prediabetic, Diabetic, and Microalbuminuria Plasma by Parallel Reaction Monitoring, SWATH, and MSE

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis

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