Mark S. Baker
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View article: Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins
Recombinant Protein Spectral Library (rPSL) DIA-MS method improves identification and quantification of low-abundance cancer-associated and kynurenine pathway proteins Open
Data-independent acquisition mass spectrometry (DIA-MS) is a powerful tool for quantitative proteomics, but a well-constructed reference spectral library is crucial to optimize DIA analysis, particularly for low-abundance proteins. In this…
View article: A review of U.S. city climate action plans
A review of U.S. city climate action plans Open
Cities are increasingly creating climate action plans (CAPs), but it is unclear what potential these have for cities to sufficiently address the climate crisis. We conducted a review of 157 CAPs published by U.S. cities between 2018 and ea…
View article: A Proteomic Examination of Plasma Extracellular Vesicles Across Colorectal Cancer Stages Uncovers Biological Insights That Potentially Improve Prognosis
A Proteomic Examination of Plasma Extracellular Vesicles Across Colorectal Cancer Stages Uncovers Biological Insights That Potentially Improve Prognosis Open
Background: Recent advancements in understanding plasma extracellular vesicles (EVs) and their role in disease biology have provided additional unique insights into the study of Colorectal Cancer (CRC). Methods: This study aimed to gain bi…
View article: Recombinant Protein Spectral Library (rPSL) DIA-MS Method Improves Identification and Quantification of Low-Abundance Cancer-Associated and Kynurenine Pathway Proteins
Recombinant Protein Spectral Library (rPSL) DIA-MS Method Improves Identification and Quantification of Low-Abundance Cancer-Associated and Kynurenine Pathway Proteins Open
Data-independent acquisition mass spectrometry (DIA-MS) is a powerful tool for quantitative proteomics, but a well-constructed reference spectral library is crucial to optimize DIA analysis, particularly for low-abundance proteins. In this…
View article: The Low-Abundance Plasma Proteome Reveals Differentially Abundant Proteins Associated with Breast Implant Capsular Contracture: A Pilot Study
The Low-Abundance Plasma Proteome Reveals Differentially Abundant Proteins Associated with Breast Implant Capsular Contracture: A Pilot Study Open
Capsular contracture (CC) is one of the most common postoperative complications associated with breast implant-associated infections. The mechanisms that lead to CC remain poorly understood. Plasma is an ideal biospecimen for early proteom…
View article: Protein prognostic biomarkers in stage II colorectal cancer: implications for post-operative management
Protein prognostic biomarkers in stage II colorectal cancer: implications for post-operative management Open
Colorectal cancer (CRC) poses a significant threat to many human lives worldwide and survival following resection is predominantly stage dependent. For early-stage cancer, patients are not routinely advised to undergo additional post-opera…
View article: Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis
Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis Open
Human infectious diseases are contributed equally by the host immune system's efficiency and any pathogens' infectivity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the coronavirus strain causing the respiratory pandemi…
View article: A Recombinant Protein Biomarker DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins
A Recombinant Protein Biomarker DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins Open
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). Here, we employed a mixture of recombinant proteins i…
View article: Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project Open
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made th…
View article: Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 Open
This FAIRsharing record describes: The Human Proteome Project (HPP) aims to encourage all participants/authors to uphold rigorous standards for publication and dissemination of results. All data are to be submitted to a ProteomeXchange pub…
View article: Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project
Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project Open
The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medici…
View article: Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 Open
The Human Proteome Organization’s (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the com…
View article: Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data Open
The proteomic analyses of human blood and blood-derived products (e.g. plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing prote…
View article: MOESM2 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
MOESM2 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel Open
Additional file 2: Table S1. List of identified proteins/peptides from different peptide fractionation methods.
View article: MOESM3 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
MOESM3 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel Open
Additional file 3: Table S2. Plasma protein concentration, subcellular location and tissue specificity.
View article: MOESM4 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
MOESM4 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel Open
Additional file 4: Table S3. List of 8 proteins that have not previously identified in human plasma, searched against PeptideAtlas database.
View article: MOESM6 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
MOESM6 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel Open
Additional file 6: Table S5. List of 37 potential CRC biomarker protein candidates.
View article: MOESM5 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel
MOESM5 of Potential early clinical stage colorectal cancer diagnosis using a proteomics blood test panel Open
Additional file 5: Table S4. List of quantifiable plasma proteins captured by non-depletion and depletion strategies.
View article: Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project
Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project Open
The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the lif…
View article: iSwathX: an interactive web-based application for extension of DIA peptide reference libraries
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries Open
Summary Large-scale peptide mass spectrometry (MS)/MS reference libraries are essential for the comprehensive analysis of data-independent acquisition (DIA) MS datasets, providing a comprehensive set of spectra for identification and quant…
View article: How many human proteoforms are there
How many human proteoforms are there Open
Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the …
View article: 17β-estradiol Changes the Human Cerebral Endothelial Cell Proteome Upon Exposure to Cyclic Stretch
17β-estradiol Changes the Human Cerebral Endothelial Cell Proteome Upon Exposure to Cyclic Stretch Open
Hypertension and estrogen deficiency in women have been identified as significant risk factors for cerebrovascular diseases. Hypertension causes excessive vascular stretch and contributes to the initiation of cellular injury in blood vesse…
View article: 17β-estradiol Changes the Human Cerebral Endothelial Cell Proteome Upon Exposure to Cyclic Stretch
17β-estradiol Changes the Human Cerebral Endothelial Cell Proteome Upon Exposure to Cyclic Stretch Open
Hypertension and estrogen deficiency in women have been identified as significant risk factors for cerebrovascular diseases. Hypertension causes excessive vascular stretch and contributes to the initiation of cellular injury in blood vesse…
View article: The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays Open
Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances…