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idX2

Second version of the idX algorithm. Implemented in C++ 17, using the idX Python project as a starting point.

A proteomics PSM assignment engine replacing most of the math with operations involving indexed collections. Identification confidence scoring based on Fisher's noncentral hypergeometric distribution, in conjunction with the number of ions matched with a sequence fragmentation pattern and the fraction of the ion intensity corresponding to those matched ions.

Current version: 2021.01 (std)

Kernels:

idX was designed to use a particular type of peptide sequence index file, which is referred to as a "kernel" file to avoid confusion with other projects that use indexing strategies. Kernel files are prepared prior to run time, so they can be edited and validated prior to use. All masses in kernels are in rounded integer millidaltons, so 1000.1231 Da would be represented as 1000123 mDa. All masses correspond to the neutral mass, not the ion mass. All references to specific residues are in protein coordinates.

These kernel files contain 3 types of entries and they are written in JSON Lines format.

  1. The first JSON line must be like:

{"format":"jsms 1.0","source":"some description","created":"2019-12-17 21:55:36.492350"}

  1. The lines containing peptide sequence information must be like (but all on 1 line):

{"lv":0,
"pm":parent mass,
"lb":"protein accession",
"pre":"residue - 1",
"post":"residue N+1",
"beg":start of peptide,
"end":end of peptide,
"seq":"peptide sequence",
"ns":[list of historical observations],
"bs":[list of b-fragment neutral masses],
"ys":[list of y-fragment neutral masses],
"mods":[list of modifications [residue,pos,mass]],
"u":uid for line,
"h":uid for peptide}

  1. The last line must be like:

{"validation":"sha256","value":"a21cd37e5ea05e36ddd264d0ede9abe108274ee7e58ad35dc08a468ff23d60bd"}

where the "value" is the SHA256 hash of all of the preceeding lines, with leading and trailing white splace removed.

Design:

The software runs using the main() method in idx.cpp to control the workflow of PSM identification. This method is also responsible for most of the logging text output that is directed to stdout. The order of operations in this method are as follows:

  1. Command line parameters are checked and stored. Use the "--help" command line option to get the current list of parameters.

  2. A load_kernel object is created and passed to a load_spectra object, that creates a list of spectra in the load_spectra object and an index of those spectra in the load_kernel object.

  3. The load_kernel object is then loaded with peptide sequence information from the kernel file specified on the command line. Only kernels that have pm values within 20 ppm of a spectrum are processed. Only information required for step 4 is stored in memory: the other kernel information required for creating a useful output file is retrieved from a reparsing of the kernel file in step 5.

  4. A create_results object is created and it uses the load_kernel and load_spectra objects to generate a preliminary set of PSM assignments. Following this step all unnecessary memory objects are released prior to advancing to step 5.

  5. A create_output object is created which takes the preliminary list of PSM assignments and applies physical and statistical models to the list, generating a final list of PSM assignments that is recorded in a tab-separated value output file as specified on the command line. In order to do this, the object re-reads the kernel file, extracting information only from the kernels in the PSM list. This reparsing of the kernel file is one of the main elements in the memory size minimization strategy. An additional metadata file in JSON format is also generated and stored at "OUTPUT_PATH.meta".

NOTE: As much as possible, neutral masses in integer millidaltons (type int32_t) are used throught the idX code, with as few variable type conversions as possible. C++ STL object indexes and sizes use type size_t as often as possible.

NOTE: The PSM identification process is performed using C++ STL maps and sets. The high performance maps and sets in parallel_hashmap are used for the largest indexed data structures.

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Second version of the idX algorithm

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