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Title: Advances in microscale separations towards nanoproteomics applications

Journal Article · · Journal of Chromatography
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  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division, Environmental Molecular Sciences Lab.

Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. But, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1 μg total proteins (e.g., cellular heterogeneity in tissue pathologies). We review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830; AC05-76RL0 1830
OSTI ID:
1390579
Alternate ID(s):
OSTI ID: 1549572
Report Number(s):
PNNL-SA-125498; PII: S0021967317310567
Journal Information:
Journal of Chromatography, Vol. 1523; ISSN 0021-9673
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 37 works
Citation information provided by
Web of Science

References (108)

The Coming Age of Complete, Accurate, and Ubiquitous Proteomes journal February 2013
Mass-spectrometric exploration of proteome structure and function journal September 2016
Advances and Challenges in Liquid Chromatography-Mass Spectrometry-based Proteomics Profiling for Clinical Applications journal October 2006
Next-generation proteomics: towards an integrative view of proteome dynamics journal December 2012
Multidimensional proteomics for cell biology journal April 2015
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer journal July 2016
Proteogenomics connects somatic mutations to signalling in breast cancer journal May 2016
Proteogenomic characterization of human colon and rectal cancer journal July 2014
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway journal July 2016
Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor journal June 2011
Comprehensive proteomics journal February 2011
Integrated proteomic analysis of post-translational modifications by serial enrichment journal June 2013
Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling journal September 2014
Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome journal October 2011
Single-cell genome sequencing: current state of the science journal January 2016
Proteomic analysis of neurons microdissected from formalin-fixed, paraffin-embedded Alzheimer’s disease brain tissue journal October 2015
Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples journal December 2016
Erratum: Corrigendum: Isolation of exosomes by differential centrifugation: Theoretical analysis of a commonly used protocol journal March 2016
Single-cell sequencing-based technologies will revolutionize whole-organism science journal July 2013
Genomic Analysis at the Single-Cell Level journal December 2011
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer journal April 2014
Progress in Top-Down Proteomics and the Analysis of Proteoforms journal June 2016
Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry journal August 1999
Protein Analysis by Shotgun/Bottom-up Proteomics journal February 2013
Mass spectrometry for proteomics journal October 2008
Analytical Properties of the Nanoelectrospray Ion Source journal January 1996
Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? journal May 2003
Ultrasensitive Proteomics Using High-Efficiency On-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS journal January 2004
Ultrasensitive and Fast Bottom-up Analysis of Femtogram Amounts of Complex Proteome Digests journal October 2013
Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last? journal September 1994
High-Efficiency Nanoscale Liquid Chromatography Coupled On-Line with Mass Spectrometry Using Nanoelectrospray Ionization for Proteomics journal August 2002
Proteomic Analysis of Ductal Carcinoma of the Breast Using Laser Capture Microdissection, LC−MS, and 16 O/ 18 O Isotopic Labeling journal June 2004
Quantitative proteomic analysis of single pancreatic islets journal October 2009
Single Cell Proteomics Using Frog ( Xenopus laevis ) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content journal June 2016
Development of Mass Spectrometry-Based Shotgun Method for Proteome Analysis of 500 to 5000 Cancer Cells journal March 2010
Low-Attomole Electrospray Ionization MS and MS/MS Analysis of Protein Tryptic Digests Using 20-μm-i.d. Polystyrene−Divinylbenzene Monolithic Capillary Columns journal October 2003
Monolithic silica columns for high-efficiency separations by high-performance liquid chromatography journal June 2002
Preparation of 20-μm-i.d. Silica-Based Monolithic Columns and Their Performance for Proteomics Analyses journal August 2005
Octadecylated Silica Monolith Capillary Column with Integrated Nanoelectrospray Ionization Emitter for Highly Efficient Proteome Analysis journal March 2006
MicroSPE-nanoLC-ESI-MS/MS Using 10-μm-i.d. Silica-Based Monolithic Columns for Proteomics journal January 2007
More Sensitive and Quantitative Proteomic Measurements Using Very Low Flow Rate Porous Silica Monolithic LC Columns with Electrospray Ionization-Mass Spectrometry journal May 2006
On-Line 1D and 2D Porous Layer Open Tubular/LC-ESI-MS Using 10-μm-i.d. Poly(styrene−divinylbenzene) Columns for Ultrasensitive Proteomic Analysis journal August 2007
Ultratrace LC/MS Proteomic Analysis Using 10-μm-i.d. Porous Layer Open Tubular Poly(styrene−divinylbenzene) Capillary Columns journal February 2007
Separation optimization of long porous-layer open-tubular columns for nano-LC-MS of limited proteomic samples: Liquid Chromatography journal September 2013
Capillary zone electrophoresis-mass spectrometry using an electrospray ionization interface journal March 1988
New insight into suction and dilution effects in CE coupled to MS via an ESI interface. II - Dilution effect journal May 2009
Simplified capillary electrophoresis nanospray sheath-flow interface for high efficiency and sensitive peptide analysis: Capillary electrophoresis electrospray interface journal July 2010
Simplifying CE−MS Operation. 2. Interfacing Low-Flow Separation Techniques to Mass Spectrometry Using a Porous Tip journal June 2007
Mass Transport in a Micro Flow-Through Vial of a Junction-at-the-Tip Capillary Electrophoresis-Mass Spectrometry Interface journal June 2011
Sheathless capillary electrophoresis electrospray ionization-mass spectrometry interface based on poly(dimethylsiloxane) membrane emitter and thin conducting liquid film: CE and CEC journal July 2013
Ultrasensitive Sample Quantitation via Selected Reaction Monitoring Using CITP/CZE–ESI-Triple Quadrupole MS journal November 2012
Quantitative Multiple Reaction Monitoring of Peptide Abundance Introduced via a Capillary Zone Electrophoresis–Electrospray Interface journal June 2012
On-line amino acid-based capillary isoelectric focusing-ESI-MS/MS for protein digests analysis journal October 2012
Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest journal January 2013
Bottom-up proteome analysis of E. coli using capillary zone electrophoresis-tandem mass spectrometry with an electrokinetic sheath-flow electrospray interface journal August 2013
Single-Shot Proteomics Using Capillary Zone Electrophoresis–Electrospray Ionization-Tandem Mass Spectrometry with Production of More than 1 250 Escherichia coli Peptide Identifications in a 50 min Separation journal February 2013
Over 10 000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry journal October 2014
Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry for quantitative parallel reaction monitoring of peptide abundance and single-shot proteomic analysis of a human cell line journal September 2014
Bottom-Up Proteomics of Escherichia coli Using Dynamic pH Junction Preconcentration and Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry journal June 2014
Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum journal September 2012
Loss-less Nano-fractionator for High Sensitivity, High Coverage Proteomics journal January 2017
Large-scale analysis of the yeast proteome by multidimensional protein identification technology journal March 2001
Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis journal November 2011
Online Nanoflow RP−RP-MS Reveals Dynamics of Multicomponent Ku Complex in Response to DNA Damage journal December 2010
Nanoflow Low Pressure High Peak Capacity Single Dimension LC-MS/MS Platform for High-Throughput, In-Depth Analysis of Mammalian Proteomes journal June 2012
Online Nanoflow Reversed Phase-Strong Anion Exchange-Reversed Phase Liquid Chromatography–Tandem Mass Spectrometry Platform for Efficient and In-Depth Proteome Sequence Analysis of Complex Organisms journal September 2011
Genome-scale proteome quantification by DEEP SEQ mass spectrometry journal July 2013
Proteomic Analysis with Integrated Multiple Dimensional Liquid Chromatography/Mass Spectrometry Based on Elution of Ion Exchange Column Using pH Steps journal September 2005
Multidimensional LC Separations in Shotgun Proteomics journal October 2008
Two-dimensional strong cation exchange/porous layer open tubular/mass spectrometry for ultratrace proteomic analysis using a 10 μm id poly(styrene- divinylbenzene) porous layer open tubular column with an on-line triphasic trapping column journal May 2008
Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method journal December 2005
Optimized nLC-MS workflow for laser capture microdissected breast cancer tissue journal June 2012
Proteomics Pipeline for Biomarker Discovery of Laser Capture Microdissected Breast Cancer Tissue journal May 2012
Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells journal February 2014
The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies journal April 2016
Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling journal April 2016
High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers journal July 2011
The Proteomic Reactor:  A Microfluidic Device for Processing Minute Amounts of Protein Prior to Mass Spectrometry Analysis journal October 2006
Spin filter–based sample preparation for shotgun proteomics journal November 2009
Comparative Reevaluation of FASP and Enhanced FASP Methods by LC–MS/MS journal February 2015
Uncovering the Proteome Response of the Master Circadian Clock to Light Using an AutoProteome System journal August 2011
Pressurized Pepsin Digestion in Proteomics journal February 2011
On-line Digestion System for Protein Characterization and Proteome Analysis journal December 2008
Integrated enzyme reactor and high resolving chromatography in “sub-chip” dimensions for sensitive protein mass spectrometry journal December 2013
Enzyme-immobilized reactors for rapid and efficient sample preparation in MS-based proteomic studies journal January 2013
Open Tubular Lab-On-Column/Mass Spectrometry for Targeted Proteomics of Nanogram Sample Amounts journal September 2014
A one-step preparation method of monolithic enzyme reactor for highly efficient sample preparation coupled to mass spectrometry-based proteomics studies journal September 2015
SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities journal March 2016
Microscale immobilized enzyme reactors in proteomics: Latest developments journal January 2014
Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses journal April 2017
In-tip nanoreactors for cancer cells proteome profiling journal January 2017
Rare Cell Proteomic Reactor Applied to Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-based Quantitative Proteomics Study of Human Embryonic Stem Cell Differentiation journal June 2010
Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis journal June 2015
Laser-capture microdissection journal June 2006
Fluorescence Activated Cell Sorting journal March 1972
Heterogeneity and Lobularity of Pancreatic Pathology in Type 1 Diabetes during the Prediabetic Phase journal July 2015
Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot journal May 2014
Single-step Enrichment by Ti4+-IMAC and Label-free Quantitation Enables In-depth Monitoring of Phosphorylation Dynamics with High Reproducibility and Temporal Resolution journal September 2014
The current state of the art of quantitative phosphoproteomics and its applications to diabetes research journal March 2016
Online Automated in Vivo Zebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo journal April 2008
Highly Robust, Automated, and Sensitive Online TiO 2 -Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster journal February 2008
Making Broad Proteome Protein Measurements in 1−5 min Using High-Speed RPLC Separations and High-Accuracy Mass Measurements journal December 2005
Target Proteomic Profiling of Frozen Pancreatic CD24+ Adenocarcinoma Tissues by Immuno-Laser Capture Microdissection and Nano-LC–MS/MS journal May 2013
Integration of Cell Lysis, Protein Extraction, and Digestion into One Step for Ultrafast Sample Preparation for Phosphoproteome Analysis journal July 2014
Hydrophilic Interaction Chromatography Using a Meter-Scale Monolithic Silica Capillary Column for Proteomics LC-MS journal March 2014
Optimization and Evaluation of a Sheathless Capillary Electrophoresis–Electrospray Ionization Mass Spectrometry Platform for Peptide Analysis: Comparison to Liquid Chromatography–Electrospray Ionization Mass Spectrometry journal October 2011
Improving the Comprehensiveness and Sensitivity of Sheathless Capillary Electrophoresis–Tandem Mass Spectrometry for Proteomic Analysis journal October 2012
Preparation of linear polyacrylamide coating and strong cationic exchange hybrid monolith in a single capillary, and its application as an automated platform for bottom-up proteomics by capillary electrophoresis-mass spectrometry journal January 2017

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Portable capillary liquid chromatography for pharmaceutical and illicit drug analysis journal February 2020
New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells journal January 2019
Recent developments and applications of capillary and microchip electrophoresis in proteomics and peptidomics (2015-mid 2018) journal November 2018
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Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy journal October 2018

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