Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

9.5K
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
9.5K
Measures of Central Tendency02:16

Measures of Central Tendency

21.1K
The "center" of a data set is also a way of describing location. The two most widely used measures of the "center" of the data are the mean (average) and the median. The words "mean" and "average" are often used interchangeably. The substitution of one word for the other is common practice. The technical term is "arithmetic mean" and "average" is technically a center location. However, in practice among non-statisticians,...
21.1K
Histone Modification02:32

Histone Modification

16.1K
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
16.1K
Self-Evaluation: Self-Enhancement and Self-Verification03:00

Self-Evaluation: Self-Enhancement and Self-Verification

5.8K
Social psychologists have documented that feeling good about ourselves and maintaining positive self-esteem is a powerful motivator of human behavior (Tavris & Aronson, 2008). In the United States, members of the predominant culture typically think very highly of themselves and view themselves as good people who are above average on many desirable traits (Ehrlinger, Gilovich, & Ross, 2005). Often, our behavior, attitudes, and beliefs are affected when we experience a threat to our...
5.8K
Sternberg's Triangular Theory of Love02:15

Sternberg's Triangular Theory of Love

45.9K
We typically love the people with whom we form relationships, but the type of love we have for our family, friends, and lovers differs. Robert Sternberg (1986) proposed that there are three components of love: intimacy, passion, and commitment. These three components form a triangle that defines multiple types of love: this is known as Sternberg’s triangular theory of love. Intimacy is the sharing of details and intimate thoughts and emotions. Passion is the physical attraction—the...
45.9K
Robbers Cave04:49

Robbers Cave

14.8K
During the 1950s, the landmark Robbers Cave experiment demonstrated that when groups must compete with one another, intergroup conflict, hostility, and even violence may result. At the Oklahoman summer camp, two troops of boys—termed the Rattlers and the Eagles—took part in a week-long tournament. During this time, their negativity culminated in derogatory name-calling, fistfights, and even vandalism and destruction of property. However, this work also revealed that such tension...
14.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Optimization of LC-ExD methods for glycopeptides on an Omnitrap-Orbitrap platform.

Analytical and bioanalytical chemistry·2026
Same author

Updates to the Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines.

Analytical and bioanalytical chemistry·2026
Same author

Overview of Proteomic Analysis of Amyloid Plaques and Neurofibrillary Tangles in Alzheimer's Disease.

Biomolecules·2025
Same author

Unveiling the Accurate Site-Specific <i>N</i>- and <i>O</i>-Glycosylation of Hyperglycosylated Erythropoietin Drugs by an Integrated Approach.

Analytical chemistry·2025
Same author

Recent analytical advances in the detection and characterization of 3-O-sulfated heparan sulfate.

Analytical and bioanalytical chemistry·2025
Same author

Untangling Heparan Sulfate 3-<i>O</i>-Sulfation Using a Novel Offline Cationic-Peptide Affinity Enrichment, Followed by HILIC-cIM-MS.

Analytical chemistry·2025
Same journal

A temporal phospho-acetylome atlas of human myogenesis identifies coordinated post-translational regulation.

Molecular & cellular proteomics : MCP·2026
Same journal

Temporal proteomic characterization of SARS-CoV-2 infected mouse lungs.

Molecular & cellular proteomics : MCP·2026
Same journal

Platelet proteome links metabolism to reactivity in Essential Thrombocythemia.

Molecular & cellular proteomics : MCP·2026
Same journal

Genetic rescue of disrupted synaptic protein interaction network dynamics following SYNGAP1 reactivation.

Molecular & cellular proteomics : MCP·2026
Same journal

ASAP-ID: Proximity labelling with small tags.

Molecular & cellular proteomics : MCP·2026
Same journal

Proteome profiling reveals NQO2 activity contributing to proteasome inhibitor resistance in multiple myeloma cell lines.

Molecular & cellular proteomics : MCP·2026
See all related articles

Related Experiment Video

Updated: Jan 31, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

13.4K

psims - A Declarative Writer for mzML and mzIdentML for Python.

Joshua Klein1, Joseph Zaia2,3

  • 1From the ‡Program for Bioinformatics, Boston University, Boston, Massachusetts 02215.

Molecular & Cellular Proteomics : MCP
|December 20, 2018
PubMed
Summary
This summary is machine-generated.

A new Python library called psims simplifies creating mass spectrometry data files (mzML and mzIdentML). This tool offers a flexible and accessible way for researchers to generate these complex scientific data formats.

Keywords:
BioinformaticsBioinformatics softwareData standardsMass SpectrometryQuality control and metricsmzIdentMLmzML

More Related Videos

Author Spotlight: High-Resolution 4D Light-Sheet Imaging and Virtual Reality in Zebrafish for Single-Cell Analysis of Heart Function
07:07

Author Spotlight: High-Resolution 4D Light-Sheet Imaging and Virtual Reality in Zebrafish for Single-Cell Analysis of Heart Function

Published on: January 5, 2024

1.9K
Miniaturized Sample Preparation for Transmission Electron Microscopy
09:04

Miniaturized Sample Preparation for Transmission Electron Microscopy

Published on: July 27, 2018

20.6K

Related Experiment Videos

Last Updated: Jan 31, 2026

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
07:38

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

13.4K
Author Spotlight: High-Resolution 4D Light-Sheet Imaging and Virtual Reality in Zebrafish for Single-Cell Analysis of Heart Function
07:07

Author Spotlight: High-Resolution 4D Light-Sheet Imaging and Virtual Reality in Zebrafish for Single-Cell Analysis of Heart Function

Published on: January 5, 2024

1.9K
Miniaturized Sample Preparation for Transmission Electron Microscopy
09:04

Miniaturized Sample Preparation for Transmission Electron Microscopy

Published on: July 27, 2018

20.6K

Area of Science:

  • * Mass Spectrometry Data Standards
  • * Bioinformatics Data Formats

Background:

  • * mzML and mzIdentML are crucial but complex formats for mass spectrometry data and identifications.
  • * Existing implementations are often in compiled languages, limiting flexibility and accessibility for scripting languages.
  • * There is a need for accessible tools to generate mzML and mzIdentML in scripting environments like Python or R.

Purpose of the Study:

  • * To introduce psims, a Python library for generating mzML and mzIdentML files.
  • * To provide a flexible and user-friendly implementation for creating these mass spectrometry data formats.
  • * To enable easier data representation and sharing in the scientific community.

Main Methods:

  • * Developed a Python library, psims, for writing mzML and mzIdentML files.
  • * Utilized built-in Python data structures for XML format generation.
  • * Incorporated a controlled vocabulary resolution system and an identity tracking system.

Main Results:

  • * psims enables the creation of mzML and mzIdentML files using Python.
  • * The library simplifies the encoding process through vocabulary resolution and identity tracking.
  • * Offers a flexible alternative to existing implementations, particularly for scripting languages.

Conclusions:

  • * psims provides a much-needed, accessible implementation for generating mass spectrometry data files.
  • * Facilitates easier data handling and integration for researchers using Python.
  • * Promotes wider adoption and interoperability of mzML and mzIdentML standards.