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pgb-liv/php-ms
==============

PHP Mass Spectrometry Utilities library

v1.0.0(8y ago)21.0kApache-2.0PHPPHP >=5.4.0CI failing

Since Nov 1Pushed 6y ago5 watchersCompare

[ Source](https://github.com/PGB-LIV/php-ms)[ Packagist](https://packagist.org/packages/pgb-liv/php-ms)[ Docs](https://github.com/PGB-LIV/php-ms)[ RSS](/packages/pgb-liv-php-ms/feed)WikiDiscussions master Synced 3w ago

READMEChangelog (1)Dependencies (7)Versions (2)Used By (0)

phpMs
=====

[](#phpms)

phpMs is PHP-based free open-source library for proteomics. The library contains a core set of classes for storing common data such as spectra, peptides and proteins. In addition the library contains a number of readers and/or writers for common file formats, including MGF, FASTA, mzIdentML, proBed. The library also contains a number of useful utilities for performing protein digestion, peptide fragmentation, and search engine integration.

[![Build Status](https://camo.githubusercontent.com/45daae4a74ad11c5c45e728189e7bd7be2d456b9ee1fa4e6b23e7c6217976ca3/687474703a2f2f7067622e6c69762e61632e756b2f6a656e6b696e732f6275696c645374617475732f69636f6e3f6a6f623d7068702d6d73)](https://camo.githubusercontent.com/45daae4a74ad11c5c45e728189e7bd7be2d456b9ee1fa4e6b23e7c6217976ca3/687474703a2f2f7067622e6c69762e61632e756b2f6a656e6b696e732f6275696c645374617475732f69636f6e3f6a6f623d7068702d6d73)[![Quality Gate](https://camo.githubusercontent.com/b3ac0131faf66ac949af56d79418ddd7f6da084276e8714d074d835f5c9c23e6/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f676174652e737667)](https://camo.githubusercontent.com/b3ac0131faf66ac949af56d79418ddd7f6da084276e8714d074d835f5c9c23e6/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f676174652e737667)

[![Test Success](https://camo.githubusercontent.com/6a6dedfef91bd99b7488140e7253908bc982b4d42c04341265ff4433893c10ca/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f746573745f737563636573735f64656e736974792e737667)](https://camo.githubusercontent.com/6a6dedfef91bd99b7488140e7253908bc982b4d42c04341265ff4433893c10ca/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f746573745f737563636573735f64656e736974792e737667)[![Unit Test Coverage](https://camo.githubusercontent.com/934f8a7221dfdd08948186febfe823257e368943507086c8b586f9fbf708a8c3/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f636f7665726167652e737667)](https://camo.githubusercontent.com/934f8a7221dfdd08948186febfe823257e368943507086c8b586f9fbf708a8c3/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f636f7665726167652e737667)[![SQALE Debt Ratio](https://camo.githubusercontent.com/e92094510de45edb02979de6f7b5353a0049adcce001c32e44183f0727b77df1/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f7371616c655f646562745f726174696f2e737667)](https://camo.githubusercontent.com/e92094510de45edb02979de6f7b5353a0049adcce001c32e44183f0727b77df1/687474703a2f2f7067622e6c69762e61632e756b2f63692f7068704d732f62616467652f7371616c655f646562745f726174696f2e737667)

Requirements
------------

[](#requirements)

- PHP Version 5.4+
    - ext/xsl

Install
-------

[](#install)

To install the library use [Composer](https://getcomposer.org/)

```
composer require pgb-liv/php-ms

```

Or add it to your existing composer.json:

```
"require" : {
    "pgb-liv/php-ms" : "1.*"
},

```

Releases made available by GitHub and the GitHub source do not include depedency code. It is recommended you always use phpMs via Composer.

API Documentation
-----------------

[](#api-documentation)

The latest version of the API is available at:

Usage Examples
--------------

[](#usage-examples)

See the [phpMs Demo Suite](http://github.com/PGB-LIV/php-ms-example) for examples of how to use the API. A live demo is also available via

###  Health Score

29

—

LowBetter than 57% of packages

Maintenance20

Infrequent updates — may be unmaintained

Popularity17

Limited adoption so far

Community9

Small or concentrated contributor base

Maturity58

Maturing project, gaining track record

 Bus Factor1

Top contributor holds 100% of commits — single point of failure

How is this calculated?**Maintenance (25%)** — Last commit recency, latest release date, and issue-to-star ratio. Uses a 2-year decay window.

**Popularity (30%)** — Total and monthly downloads, GitHub stars, and forks. Logarithmic scaling prevents top-heavy scores.

**Community (15%)** — Contributors, dependents, forks, watchers, and maintainers. Measures real ecosystem engagement.

**Maturity (30%)** — Project age, version count, PHP version support, and release stability.

###  Release Activity

Cadence

Unknown

Total

1

Last Release

3156d ago

### Community

Maintainers

![](https://www.gravatar.com/avatar/d3e51daaa84f53c8a7241dab6f7452861eea960c0c332ab268ed9fde106499d8?d=identicon)[detritus](/maintainers/detritus)

---

Top Contributors

[![liv-acollins](https://avatars.githubusercontent.com/u/1191435?v=4)](https://github.com/liv-acollins "liv-acollins (289 commits)")

---

Tags

bioinformaticslcmsmass-spectrometryphpproteomicslcmsmsmsmsmassspec

###  Code Quality

TestsPHPUnit

Code StylePHP\_CodeSniffer

### Embed Badge

![Health badge](/badges/pgb-liv-php-ms/health.svg)

```
[![Health](https://phpackages.com/badges/pgb-liv-php-ms/health.svg)](https://phpackages.com/packages/pgb-liv-php-ms)
```

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