scholarly journals Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality

2021 ◽  
Author(s):  
James A. Sanford ◽  
Yang Wang ◽  
Joshua R. Hansen ◽  
Marina A. Gritsenko ◽  
Karl K. Weitz ◽  
...  
Keyword(s):  
Data Quality ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Peptide Loading ◽  
Mass Tag

scholarly journals Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality

2020 ◽  
Author(s):  
James A Sanford ◽  
Yang Wang ◽  
Joshua R Hansen ◽  
Marina A Gritsenko ◽  
Karl K Weitz ◽  
...  
Keyword(s):  
Data Quality ◽  
Missing Values ◽  
Clinical Proteomics ◽  
Tissue Type ◽  
Tandem Mass ◽  
Major Barrier ◽  
Tandem Mass Tag ◽  
Peptide Loading ◽  
The Impact ◽  
Mass Tag

Abstract Background: Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One major barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics—currently on the order of 25 mg wet tissue weight, depending on tissue type. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is in excess of 10 million (1E7) peripheral blood mononuclear cells (PBMCs). Throughout the course of a prospective study, this requirement will certainly exceed what is obtainable from many of the individual patients/timepoints. For this reason, we were interested in examining the impact of differential peptide loading across multiplex channels on proteomic data quality. Methods: To achieve this, we tested a range of channel loading amounts (20, 40, 100, 200, and 400 μg of tryptic peptides, or approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification reproducibility and accuracy in experiments utilizing isobaric tandem mass tag (TMT) labeling. Results: As expected, we found that fewer missing values are observed in TMT channels with higher peptide loading amounts compared to those with lower loading. Moreover, channels with lower loading amounts have greater quantitative variability than channels with higher loading amounts. Statistical analysis of the differences in means among the five loading groups showed that the 20 μg loading group was significantly different from the 400 μg loading group. However, no significant differences were detected among the 40, 100, 200 and 400 μg loading groups. Conclusions: These assessment data demonstrate the practical limits of loading differential quantities of peptides across channels in TMT multiplexes, and provide a basis for designing the optimal clinical proteomics study when specimen quantities are limited.

scholarly journals Evaluation of differential peptide loading on tandem mass tag-based proteomic and phosphoproteomic data quality

2020 ◽  
Author(s):  
James A Sanford ◽  
Yang Wang ◽  
Joshua R Hansen ◽  
Marina A Gritsenko ◽  
Karl K Weitz ◽  
...  
Keyword(s):  
Data Quality ◽  
Missing Values ◽  
Clinical Proteomics ◽  
Tissue Type ◽  
Tandem Mass ◽  
Major Barrier ◽  
Tandem Mass Tag ◽  
Peptide Loading ◽  
The Impact ◽  
Mass Tag

Abstract Background: Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One major barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics—currently on the order of 25 mg wet tissue weight, depending on tissue type. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is in excess of 10 million (1E7) peripheral blood mononuclear cells (PBMCs). Throughout the course of a prospective study, this requirement will certainly exceed what is obtainable from many of the individual patients/timepoints. For this reason, we were interested in examining the impact of differential peptide loading across multiplex channels on proteomic data quality. Methods: To achieve this, we tested a range of channel loading amounts (20, 40, 100, 200, and 400 μg of tryptic peptides, or approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification precision, and peptide/phosphopeptide detection in experiments utilizing isobaric tandem mass tag (TMT) labeling. Results: As expected, we found that fewer missing values are observed in TMT channels with higher peptide loading amounts compared to those with lower loading. Moreover, channels with lower loading amounts have greater quantitative variability than channels with higher loading amounts. Statistical analysis of the differences in means among the five loading groups showed that the 20 μg loading group was significantly different from the 400 μg loading group. However, no significant differences were detected among the 40, 100, 200 and 400 μg loading groups. Conclusions: These assessment data demonstrate the practical limits of loading differential quantities of peptides across channels in TMT multiplexes, and provide a basis for designing the optimal clinical proteomics study when specimen quantities are limited.

scholarly journals Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling

2021 ◽  
Author(s):  
Dahang Yu ◽  
Zhe Wang ◽  
Kellye A. Cupp-Sutton ◽  
Yanting Guo ◽  
Qiang Kou ◽  
...  
Keyword(s):  
Protein Level ◽  
Tandem Mass ◽  
Top Down ◽  
Complex Samples ◽  
Tandem Mass Tag ◽  
Mass Tag

scholarly journals Tandem Mass Tag-Based Quantitative Proteomics and Virulence Phenotype of Hemolymph-Treated Bacillus thuringiensis kurstaki Cells Reveal New Insights on Bacterial Pathogenesis in Insects

2021 ◽  
Author(s):  
Yanyan Sun ◽  
Linlin Yang ◽  
Lianet Rodríguez-Cabrera ◽  
Yushan Ding ◽  
Chaoliang Leng ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Quantitative Proteomics ◽  
Bacterial Pathogenesis ◽  
Midgut Epithelium ◽  
Tandem Mass ◽  
Content Type ◽  
Virulence Phenotype ◽  
Bacillus Thuringiensis Kurstaki ◽  
Tandem Mass Tag ◽  
Mass Tag

After ingestion by a susceptible insect and damaging its midgut epithelium, the bacterium Bacillus thuringiensis (Bt) reaches the insect blood (hemolymph), where it propagates despite the host’s antimicrobial defenses and induces insect death by acute septicemia. Although the hemolymph stage of the Bt toxic pathway is determinant for the infested insects’ fate, the response of Bt to hemolymph and the latter’s role in bacterial pathogenesis has been poorly explored.

Tandem mass tag-based quantitative proteomics analyses reveal the response of Bacillus licheniformis to high growth temperatures

2017 ◽  
Vol 67 (7) ◽  
pp. 501-510 ◽  
Author(s):  
Zixing Dong ◽  
Zhixin Chen ◽  
Hongbin Wang ◽  
Kangming Tian ◽  
Peng Jin ◽  
...  
Keyword(s):  
Bacillus Licheniformis ◽  
Quantitative Proteomics ◽  
High Growth ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Mass Tag

scholarly journals Data for Tandem Mass Tag (TMT) proteomic analysis of the pancreas during the early phase of experimental pancreatitis

Data in Brief ◽  
2018 ◽  
Vol 20 ◽  
pp. 779-783
Author(s):  
Violeta García-Hernández ◽  
Carmen Sánchez-Bernal ◽  
Domitille Schvartz ◽  
José J. Calvo ◽  
Jean-Charles Sanchez ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Early Phase ◽  
Experimental Pancreatitis ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Mass Tag
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