Miscellaneous

What is LFQ intensity?

What is LFQ intensity?

LFQ (label-free quantitation) intensity is a very similar to the iBAQ intensity but the protein intensities are normalized to exculde some “outliers” to best represent the ratio changes of different samples.

What is LFQ proteomics?

Relative label-free quantification (LFQ) of shotgun proteomics data using precursor (MS1) signal intensities is one of the most commonly used applications to comprehensively and globally quantify proteins across biological samples and conditions.

What is a razor peptide?

A razor peptide is a peptide that has been assigned to the Protein Group with the largest number of total peptide identified (IDs). If the razor peptide is also unique it only matches to this single Protein Group. If it is not unique, it will only be a razor peptide for the group with the largest number of peptide IDs.

What is spectral count mass spec?

Spectral count, defined as the total number of spectra identified for a protein, has gained acceptance as a practical, label-free, semiquantitative measure of protein abundance in proteomic studies.

What is a unique peptide?

A unique peptide is defined as a peptide, irrespective of its length, that exists only in one protein of a proteome of interest, despite the fact that this peptide may appear more than once in the same protein.

What is unique peptide count?

# Unique Peptides The number of peptide sequences that are unique to a protein group. These are the peptides that are common to the proteins of a protein group, and which do not occur in the proteins of any other group. The number of unique peptides that determine a protein group can be set in Proteome Discoverer.

What is label-free detection?

Label-free detection (also label-free (LF) technology, label-free analysis or label-free sensing) uses optics-based biosensors to convert biological binding responses into signals without using a fluorescent or any other detection label.

What is total spectrum count?

Total Spectrum Count – The total number of spectra associated to a single protein group, including those shared with other proteins.

What is Proteotypic peptide?

Proteotypic peptides are those peptides in a protein sequence that are most likely to be confidently observed by current MS-based proteomics methods. Libraries of proteotypic peptide sequences were compiled from the Global Proteome Machine Database for Homo sapiens and Saccharomyces cerevisiae model species proteomes.

What is PSM peptide?

A peptide-spectrum match (PSM) scoring function assigns a numerical value to a peptide-spectrum pair (P,S) expressing the likelihood that the fragmentation of a peptide with sequence P is recorded in the experimental mass spectrum S.

What is PEP score?

The PEP score is the probability that a peptide (PSM-peptide spectral match) is incorrect. The Sequest score is a calculation that scores and sums each peptide for a given protein. Basically, the higher the score the more confidence you can have that the given peptide identification is correct.

What is the difference between Ibaq and LFQ intensity?

LFQ (label-free quantitation) intensity is a very similar to the iBAQ intensity but the protein intensities are normalized to exculde some “outliers” to best represent the ratio changes of different samples. Untargeted label-free quantitation (LFQ) of proteins, aims to determine the relative amount of proteins in two or more biological samples.

What is the difference between MaxQuant and ptxqc?

Quantification will be performed using razor and unique peptides, including those modified by acetylation (protein N-terminal), oxidation (Met) and deamidation (NQ). PTXQC is used for general quality control of proteomics data, which takes MaxQuant result files.

What is maxlfq and how does it work?

We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the presence of quantifiable peptides varies from sample to sample.

How to overcome the obstacle of missing LFQ values?

To overcome the obstacle of missing LFQ values, missing values are imputed before fit the models. Hierarchical clustering is performed on Z-score normalized, log2-transformed LFQ intensities. Log ratios are calculated as the difference in average log2 LFQ intensity values between experimental and control groups.