Turning LCMS data into biological insight is essentially a well practiced operation, however inconsistent. Several tools exist to extract molecular information and re-construct protein sequences, but the processes vary from tool to tool. We provide a concise method for translating label-free proteomics into biological meaning which can be easily analyzed, searched and explored.

Product Summary

Label-free proteomics analaysis pipeline is the complete solution for transforming analytical measurements into biological observations.


There are a pluthera of choices avaiable for proteomic data analysis. However, there lacks a complete solution for label-free discovery proteomics. Mainly there exists a collection of various single step tools, utilizing custom data formats and not easily ported to third part software. SoCal Bioinformatics has over a decade developing industrial bioinformatics pipelines and we are applying that expertise to this product.This is a complete solution from raw data to biomarkers.


MS1 #

Extract MS1 molecular features from data that will later be used as the quantitative value. Futher assess the level of cation adduction, and determe the presenece of top PTMs by aggregate mass shifts.

MS2 #

Process MS2 spectra by assessing quality, re-determining the isolated mono-isotopic ion mass and charge, and calculating the level of possible secondary ion contamination.

Peptides #

Employing a proteomic search engine designed to account for multiple PTMs, known amino acid polymorphisms, and gene products. The Uniprot UniREF database is utilized to include all known protein variants, a genome translation can also be included.

Proteins #

Protein accounting while considering homology and variable amin acid polymorphisms. This can be extend to all study related experimets, simultaneously applying a process for peptide inferencing between experiments to increas biological coverage.

Mapping #

The final stage of the analysis is to map peptide identificiations to neutral mass molecular features.


Product Deliverable

Password protected account to access HDF5 files for downloading, and or CSV table extracts. An SQL supported web portal for data exploration and supporting analysis reports.