Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues

2017 ◽  
pp. 123-133 ◽  
Author(s):  
Gaoyuan Song ◽  
Maxwell R. McReynolds ◽  
Justin W. Walley
Keyword(s):  
Sample Preparation ◽  
Plant Tissues ◽  
Protein Abundance

Effect of Sample Preparation Methods on Analytical Values of Some Micro‐ and Secondary Nutrients in Plant Tissues

2008 ◽  
Vol 39 (13-14) ◽  
pp. 2046-2052 ◽  
Author(s):  
Prashant Srivastava ◽  
Prakash C. Srivastava ◽  
Upasana Srivastava ◽  
Uma S. Singh
Keyword(s):  
Sample Preparation ◽  
Plant Tissues ◽  
Preparation Methods ◽  
Sample Preparation Methods

scholarly journals Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics

2019 ◽  
Author(s):  
Lindsay K Pino ◽  
Han-Yin Yang ◽  
William Stafford Noble ◽  
Brian C Searle ◽  
Andrew N Hoofnagle ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Quantitative Proteomics ◽  
Protein Abundance ◽  
Complex Samples ◽  
Figures Of Merit ◽  
Data Independent Acquisition ◽  
Proteomics Experiment ◽  
Series Of Experiments ◽  
Analytical Figures Of Merit

AbstractMass spectrometry is a powerful tool for quantifying protein abundance in complex samples. Advances in sample preparation and the development of data independent acquisition (DIA) mass spectrometry approaches have increased the number of peptides and proteins measured per sample. Here we present a series of experiments demonstrating how to assess whether a peptide measurement is quantitative by mass spectrometry. Our results demonstrate that increasing the number of detected peptides in a proteomics experiment does not necessarily result in increased numbers of peptides that can be measured quantitatively.

scholarly journals Article Commentary: How Many Proteins are Missed in Quantitative Proteomics Based on MS/MS Sequencing Methods?

2010 ◽  
Vol 3 ◽  
pp. PRI.S5882 ◽  
Author(s):  
Claire Mulvey ◽  
Bettina Thur ◽  
Mark Crawford ◽  
Jasminka Godovac-Zimmermann
Keyword(s):  
Breast Cancer ◽  
Sample Preparation ◽  
Quantitative Proteomics ◽  
Breast Cancer Cells ◽  
Protein Abundance ◽  
Spectral Counting ◽  
Proteome Coverage ◽  
Counting Methods ◽  
Spectral Counts ◽  
Mcf 7

Current bottom-up quantitative proteomics methods based on MS/MS sequencing of peptides are shown to be strongly dependent on sample preparation. Using cytosolic proteins from MCF-7 breast cancer cells, it is shown that protein pre-fractionation based on pI and MW is more effective than pre-fractionation using only MW in increasing the number of observed proteins (947 vs. 704 proteins) and the number of spectral counts per protein. Combination of MS data from the different pre-fractionation methods results in further improvements (1238 proteins). We discuss that at present the main limitation on quantitation by MS/MS sequencing is not MS sensitivity and protein abundance, but rather extensive peptide overlap and limited MS/MS sequencing throughput, and that this favors internally calibrated methods such as SILAC, ICAT or ITRAQ over spectral counting methods in attempts to drastically improve proteome coverage of biological samples.

scholarly journals Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review

2016 ◽  
Vol 7 ◽  
Author(s):  
Yonghui Dong ◽  
Bin Li ◽  
Sergey Malitsky ◽  
Ilana Rogachev ◽  
Asaph Aharoni ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sample Preparation ◽  
Mass Spectrometry Imaging ◽  
Plant Tissues

Pollutant Identification by Selected Area Electron Diffraction

1974 ◽  
Vol 32 ◽  
pp. 532-533
Author(s):  
R. E. Ferrell ◽  
G. G. Paulson ◽  
C. W. Walker
Keyword(s):  
Thermal Treatment ◽  
Electron Diffraction ◽  
Sample Preparation ◽  
Crystal Structures ◽  
Water Samples ◽  
Environmental Samples ◽  
Short Review ◽  
Selected Area Electron Diffraction ◽  
Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

Preparation of Thin Cadmium Telluride Samples for Electron Microscope Studies

1974 ◽  
Vol 32 ◽  
pp. 548-549
Author(s):  
T. J. Magee ◽  
J. Peng ◽  
J. Bean
Keyword(s):  
Electron Microscope ◽  
Sulfuric Acid ◽  
Solid State ◽  
Sample Preparation ◽  
Cadmium Telluride ◽  
Potassium Dichromate ◽  
Optical Components ◽  
The Past ◽  
Solid State Devices

Cadmium telluride has become increasingly important in a number of technological applications, particularly in the area of laser-optical components and solid state devices, Microstructural characterizations of the material have in the past been somewhat limited because of the lack of suitable sample preparation and thinning techniques. Utilizing a modified jet thinning apparatus and a potassium dichromate-sulfuric acid thinning solution, a procedure has now been developed for obtaining thin contamination-free samples for TEM examination.

A Freeze Shadow Technique for the Preparation of Soft Paint Latexes for Electron Microscopy

1977 ◽  
Vol 35 ◽  
pp. 314-315
Author(s):  
Earl R. Walter ◽  
Glen H. Bryant
Keyword(s):  
Sample Preparation ◽  
High Vacuum ◽  
Vacuum System ◽  
Latex Particles ◽  
New Methods ◽  
Diffusion Pump ◽  
Film Forming ◽  
Routine Basis ◽  
Distribution Studies ◽  
Preparation Techniques

With the development of soft, film forming latexes for use in paints and other coatings applications, it became desirable to develop new methods of sample preparation for latex particle size distribution studies with the electron microscope. Conventional latex sample preparation techniques were inadequate due to the pronounced tendency of these new soft latex particles to distort, flatten and fuse on the substrate when they dried. In order to avoid these complications and obtain electron micrographs of undistorted latex particles of soft resins, a freeze-dry, cold shadowing technique was developed. The method has now been used in our laboratory on a routine basis for several years.The cold shadowing is done in a specially constructed vacuum system, having a conventional mechanical fore pump and oil diffusion pump supplying vacuum. The system incorporates bellows type high vacuum valves to permit a prepump cycle and opening of the shadowing chamber without shutting down the oil diffusion pump. A baffeled sorption trap isolates the shadowing chamber from the pumps.

SEM evaluation of the TEM cold-stage double-film specimen

1984 ◽  
Vol 42 ◽  
pp. 272-273
Author(s):  
Jayesh Bellare
Keyword(s):  
Spatial Distribution ◽  
Sample Preparation ◽  
Sample Thickness ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Liquid Sample ◽  
Thin Specimen ◽  
Sample Preparation Technique ◽  
Cold Stage ◽  
Film Specimen

Seeing is believing, but only after the sample preparation technique has received a systematic study and a full record is made of the treatment the sample gets.For microstructured liquids and suspensions, fast-freeze thermal fixation and cold-stage microscopy is perhaps the least artifact-laden technique. In the double-film specimen preparation technique, a layer of liquid sample is trapped between 100- and 400-mesh polymer (polyimide, PI) coated grids. Blotting against filter paper drains excess liquid and provides a thin specimen, which is fast-frozen by plunging into liquid nitrogen. This frozen sandwich (Fig. 1) is mounted in a cooling holder and viewed in TEM.Though extremely promising for visualization of liquid microstructures, this double-film technique suffers from a) ireproducibility and nonuniformity of sample thickness, b) low yield of imageable grid squares and c) nonuniform spatial distribution of particulates, which results in fewer being imaged.

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