Protein Analysis FAQ

• • Why Use Tumor Tissue and Adjacent Non-Tumor Tissue for Sequencing

  In tumor research, it is common practice to collect both tumor tissue and adjacent non-tumor tissue for sequencing. The primary reasons are as follows: 1. Comparative Analysis By comparing the genomic sequences of tumor tissue with those of adjacent non-tumor tissue, researchers can more accurately identify tumor-specific genetic alterations. Adjacent non-tumor tissue serves as a relatively normal reference, facilitating the identification of mutations that are directly implicated in tumor initiation and...

• • Why Is Nuclear Magnetic Resonance (NMR) Infrequently Employed for Qualitative and Quantitative Analysis of Amino Acids

  Nuclear Magnetic Resonance (NMR) is a highly powerful and information-dense analytical technique. However, its limited application in the qualitative and quantitative analysis of amino acids can primarily be attributed to the following factors: 1. Sensitivity In comparison with other commonly adopted techniques for amino acid analysis—such as liquid chromatography–mass spectrometry (LC-MS) and high-performance liquid chromatography (HPLC)—NMR exhibits inherently lower sensitivity. It generally requires.....

• • What Are the Causes of Negative Integrated Peak Area in High Performance Liquid Chromatography

  In High Performance Liquid Chromatography (HPLC), the integrated peak area should always be positive, as it reflects the quantity of a compound represented by the area under the chromatographic peak. A negative integrated peak area may arise due to the following reasons: 1. Excessively Broad Peak If a chromatographic peak is too broad, it may result in a negative integrated peak area. This can occur when the peak extends significantly beyond the baseline estimation region, causing the integration ..........

• • What Is the Maximum Temperature That Can Be Set for the Injection Port in Gas Chromatography-Tandem Mass Spectrometry

  The injection port temperature in gas chromatography-tandem mass spectrometry (GC-MS/MS) is primarily determined by the instrument's design and the specifications provided by the manufacturer. The allowable temperature range of the injection port may vary depending on the specific model of the gas chromatographic system. In general, the injection port temperature is adjustable within a defined range, with most commercial systems permitting settings between 40 °C and 350 °C.

• • How Is a Polypeptide Defined? What Amino Acid Length Is Considered a Polypeptide

  Polypeptides are biological macromolecules composed of several to hundreds of amino acids linked by peptide bonds. They serve as the fundamental building blocks of proteins. While there is no universally accepted definition based strictly on amino acid length, polypeptides and proteins are generally distinguished by the number of amino acid residues they contain. Typically, macromolecules consisting of 50 or fewer amino acids are referred to as polypeptides. This distinction is primarily based on two main..

• • How to Address Internal Standard Detection Failure in Positive Ion Mode During LC-MS Quantification

  In liquid chromatography-mass spectrometry (LC-MS) analysis, if an internal standard is detectable in negative ion mode but fails to appear in positive ion mode, the following factors may be responsible: 1. Chemical Properties of the Internal Standard The internal standard may not undergo efficient ionization under positive ion mode conditions. Consider selecting an alternative internal standard that is more amenable to ionization in positive ion mode. 2. Ion Source Conditions Adjust the ion source ........

• • What Are the Applications of Proteomics in the Field of Biology

  Proteomics, the large-scale study of all proteins within a biological system, represents a critical branch of biology, medicine, drug development, and other related disciplines. In biology, proteomics has been widely applied in the following areas: 1. Protein Identification Proteomics enables the identification of protein abundance, types, and post-translational modifications. Using mass spectrometry, researchers can analyze complex protein mixtures to determine amino acid sequences, structural ........

• • How to Analyze Proteomic Mass Spectrometry with MaxQuant

  MaxQuant is a widely used software platform for the analysis of proteomic mass spectrometry data. It is designed to process bottom-up proteomic data, enabling both protein identification and quantification. The following outlines the essential steps for analyzing proteomic mass spectrometry data using MaxQuant: 1. Prepare Data and Software Ensure that the latest version of MaxQuant is installed (available at: https://www.maxquant.org/). Prepare the raw mass spectrometry data files (typically in .raw format)

• • Is Protein Expression in Phosphoproteomics Related to Phosphorylation Level or Protein Activity

  Phosphoproteomics is a technique for investigating protein phosphorylation modifications, providing insights into cellular signaling, regulatory mechanisms, and protein function. In phosphoproteomics, protein expression typically refers to the total abundance of a given protein, whereas phosphorylation level denotes the relative occupancy of phosphorylation sites within the protein. Protein activity, defined as the functional capacity of the protein in vivo, may be modulated by phosphorylation events.

• • What Are the Applications of Hydrophilic Interaction Liquid Chromatography in Proteomics

  Hydrophilic Interaction Liquid Chromatography (HILIC), a variant of High-Performance Liquid Chromatography (HPLC), is primarily employed for the separation of polar compounds. Owing to its unique separation mechanism, HILIC has emerged as a powerful tool in proteomic analysis and the investigation of complex biological samples. In the context of proteomics, HILIC finds application in the following key areas: 1. Peptide Enrichment HILIC enables efficient enrichment and separation of polar peptides within....