PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues

Mohammed, Yassene; Bhowmick, Pallab; Smith, Derek; Domański, Dominik; Jackson, Angela; Michaud, Sarah; Malchow, Sebastian; Percy, Andrew J.; Chambers, Andrew G.; Palmer, Andrea L.; Zhang, Suping; Sickmann, Albert; Borchers, Christoph H.

doi:10.1002/pmic.201600210

Cited by 23 publications

(37 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…SIS peptides, which were used as internal standards, were synthesized and purified at the UVic‐Genome BC Proteomics Centre (BC, Canada). Their concentrations were determined as previously described . Of the 122 SIS peptides, five were synthesized in the heavy version of [ 13 C 6 ]Lys‐coded peptides, while 66 and 51 were synthesized as [ 13 C 6 15 N 2 ]Lys‐ and [ 13 C 6 15 N 4 ]Arg‐coded peptides, respectively (Supporting Information, Table 1).…”

Section: Methodsmentioning

confidence: 99%

Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring‐Mass Spectrometry

Hsiao

Chu

Chen

et al. 2018

Proteomics Clinical Apps

View full text Add to dashboard Cite

show abstract

Section: Methodsmentioning

confidence: 99%

Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring‐Mass Spectrometry

Hsiao

Chu

Chen

et al. 2018

Proteomics Clinical Apps

View full text Add to dashboard Cite

show abstract

“…The selection of peptides and interference-free transitions is also crucial for protein quantification. Various resources are available including PeptidePicker15, PeptideTracker16, SRMAtlas1718, PeptideAtlas18, PASSEL18 and Passport Protein Assay Portal. These tools assist researchers by assembling publically available experimental data into databases.…”

mentioning

confidence: 99%

Towards reproducible MRM based biomarker discovery using dried blood spots

Özcan

Cooper

Lago

et al. 2017

Sci Rep

View full text Add to dashboard Cite

There is an increasing interest in the use of dried blood spot (DBS) sampling and multiple reaction monitoring in proteomics. Although several groups have explored the utility of DBS by focusing on protein detection, the reproducibility of the approach and whether it can be used for biomarker discovery in high throughput studies is yet to be determined. We assessed the reproducibility of multiplexed targeted protein measurements in DBS compared to serum. Eighty-two medium to high abundance proteins were monitored in a number of technical and biological replicates. Importantly, as part of the data analysis, several statistical quality control approaches were evaluated to detect inaccurate transitions. After implementing statistical quality control measures, the median CV on the original scale for all detected peptides in DBS was 13.2% and in Serum 8.8%. We also found a strong correlation (r = 0.72) between relative peptide abundance measured in DBS and serum. The combination of minimally invasive sample collection with a highly specific and sensitive mass spectrometry (MS) technique allows for targeted quantification of multiple proteins in a single MS run. This approach has the potential to fundamentally change clinical proteomics and personalized medicine by facilitating large-scale studies.

show abstract

“…The surrogate peptides for the assays were selected by PeptidePicker and synthesized at the University of Victoria Proteomics Centre. The sample preparation protocol was developed previously and is available from PeptideTracker . Briefly, for the current study, the sample digests were prepared through denaturation and reduction of the homogenate with 9M urea/20mM dithiothreitol for 30 minutes at 37ºC.…”

Section: Methodsmentioning

confidence: 99%

“…The sample preparation protocol was developed previously 13,17 and is available from PeptideTracker. 15 Briefly, for the current study, the sample digests were prepared through denaturation and reduction of the homogenate with 9M urea/20mM dithiothreitol for 30 minutes at 37ºC. Denatured proteins were alkylated with iodoacetamide (40 mM final concentration) for 30 minutes at room temperature, and then samples were diluted to reach a final urea concentration of 0.55 mM prior to tryptic digestion.…”

Section: Targeted Quantitative Proteomicsmentioning

confidence: 99%

The intestinal microbiome potentially affects thrombin generation in human subjects

Mohammed

Kootte

Kopatz

et al. 2020

Journal of Thrombosis and Haemostasis

Self Cite

View full text Add to dashboard Cite

Background The intestinal microbiome plays a versatile role in the etiology of arterial thrombosis. In venous thrombosis, driven chiefly by plasma coagulation, no such role has yet been established. We hypothesized that the intestinal microbiome composition affects coagulation in humans. Methods We used healthy donor fecal microbiota transplant (FMT) to experimentally change the microbiome composition in metabolic syndrome patients. Thirty‐five subjects were randomized in a blinded fashion to healthy donor FMT or autologous FMT as a control in a 2:1 ratio. We measured thrombin generation at baseline and after 6 weeks using automated calibrated thrombinography, and we determined plasma abundance of 32 coagulation related proteins using a targeted mass spectrometry‐based quantitative proteomics assay with heavy labeled internal standards. Results Healthy donor FMT prolonged the thrombinography lag time (median delta 0.0 versus 0.25 minutes, P = .039). The other thrombinography parameters showed no significant difference. Unsupervised cluster analysis suggested overall downregulation of coagulation related plasma proteins in subject clusters containing predominantly subjects that had a metabolic response to healthy donor FMT. FMT treatment status itself showed no clear clustering pattern with up‐ or downregulation, however, and proteins did not cluster according to an apparent biological grouping. Discussion A single healthy donor FMT tends to modestly suppress the onset thrombin generation in metabolic syndrome patients, representing initial proof‐of‐principle that the intestinal microbiota composition might affect the coagulation system in humans. The findings merit external validation as a role for intestinal microbiota in coagulation can have clinically important implications.

show abstract

PeptideTracker: A knowledge base for collecting and storing information on protein concentrations in biological tissues

Cited by 23 publications

References 22 publications

Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring‐Mass Spectrometry

Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring‐Mass Spectrometry

Towards reproducible MRM based biomarker discovery using dried blood spots

The intestinal microbiome potentially affects thrombin generation in human subjects

Contact Info

Product

Resources

About