cortado-ms 0.16.3

Confidence estimation for extreme-scale proteomics experiments

cortado is a Python package that implements various methods to estimate false discovery rates (FDR) in extreme-scale mass spectrometry proteomics experiments. cortado is focused on gathering and reducing datasets to enable applying efficient implementations to estimate FDR. An additional focus is supporting peptide-centric searching through the "mixture-maximum" (MixMax) approach, which also supports spectrum-centric searches.

Cortado is designed to be easy-to-use and flexible. Currently the following modes are supported:

• Global PSM FDR
• Global peptide or precursor FDR
• MixMax q-value estimation
• Protein scoring by rolling up PSM scores
• Protein q-value estimation

Installation

cortado requires Python 3.8+ and can be installed with pip:

pip install cortado-ms

Basic Usage

Using cortado requires that you collect a dataset of PSMs, which can easily be accomplished with the wheely-mammoth library, which is installed when you install cortado-ms:

>>> from wheely.mammoth.parsers import read_encyclopedia_features
>>> ds = read_encyclopedia_features("data/*.features.txt")

You can then compute q-values using the assign_confidence function:

>>> from cortado import assign_confidence
>>> conf = assign_confidence(ds, "primary", desc=False)
>>> print(f"pi0={100*conf.pi0:.2f}%")
pi0=36.74%
>>> conf.data.toPandas()[["primary", "sequence", "q-value"]]
       primary                                           sequence   q-value
0    43.783160                             -.LSLEGDHSTPPSAYGSVK.-  0.000000
1    41.212322                           -.NGPLEVAGAAVSAGHGLPAK.-  0.000000
2    36.081665                               -.IMDPNIVGSEHYDVAR.-  0.000000
3    34.730186                  -.TTHYTPLAC[+57.0214635]GSNPLKR.-  0.000000
4    34.666630                             -.SGPKPFSAPKPQTSPSPK.-  0.000000
..         ...                                                ...       ...
827   8.150498                                     -.FGVEQDRMDK.-  0.414025
828   8.065474                                     -.QYYYSADGSR.-  0.416572
829   8.028464                                     -.APHDFQFVQK.-  0.416572
830   7.946067                                     -.KLYEDAQMAR.-  0.417337
831   7.632076  -.LTC[+57.0214635]PC[+57.0214635]C[+57.0214635...  0.420368

[832 rows x 3 columns]