SAMPEI 0.0.9

SAMPEI

SAMPEI

Summary

Recent studies have revealed diverse amino acid, post-translational and non-canonical modifications of proteins in diverse organisms and tissues. However, their detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for Spectral Alignment-based Modified PEptide Identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of sub-stoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI’s robust parameterization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules.

Tandem mass spectrometry enables high-throughput peptide identifications in complex biological specimens. In conventional methods, peptide identification relies on database search which is limited by the identification of only small number of post translational modifications (less than 3). Such methods are unable to identify unanticipated PTMs. Here we developed SAMPEI, a computational method leveraging high resolution query spectra within the same or different dataset to assign target spectra with peptide sequence and unanticipated modifications (mass shift). Prior to SAMPEI, we utilized database search (X!tandem) to assign spectra with peptide sequences in each sample. Only spectra with unique modifications and with the highest peptide identification confidence (lowest e value) are selected as queries. SAMPEI then performs a series of orthogonal measures to evaluate the similarity between all unassigned spectra and query spectra within predefined mass difference window (default = +/- 200 Dalton). First, SAMPEI aligns discrete m/z ranges within unassigned spectra to the query spectra. The proportion of matched MS2 ion intensity from query over the total MS2 intensity defined as matched query intensity is used to pre-select candidate spectra. Then, two additional measures to assess the quality of the assignment against query peptide sequence are determined to evaluate the goodness of the match. Specifically, the proportion of the MS2 intensity of target spectrum matched to the theoretical m/z of the query peptide sequence over the total MS2 intensity in the target scan is one of the measures. Finally, the proportion of the largest consecutive b/y ions missing over the length of the peptide sequence defined as largest gap percentage is the last measure. These parameters can be adjusted to maximize sensitivity or specificity, as dictated by experimental needs.

Figure 1. Schematcis of SAMPEI. (A) Example spectra represent the naive and modified peptide where Dm denotes the potential modification at residue F. With database (DB) search, only defined modification is able to be identified (Top). When incorporating DB search with SAMPEI, high quality query spectra was leveraged to identify target spectra with high similarities through three measures, matched query intensity, matched peptide intensity and largest gap percentage

Installation

SAMPEI can be installed using either pip or conda.

Conda

1. If Anaconda is not installed, first install it by following instructions found here: https://docs.conda.io/en/latest/miniconda.html

2. Install the package using : conda install -c bioconda sampei

Pip

1. Pip is generally installed with Python
2. Install the package using pip install sampei

Usage

Once installed SAMPEI can be run using the sampei command in the terminal.

To ensure that the package has been installed and to view the command line arguments run: sampei --help

This command will ouput the command line help if the package has been installed correctly.

Running SAMPEI

Once sampei has been installed it can be run using the following command:

sampei <<query_mgf_file_path>> <<target_mgf_file_path>> <<id_file_path>> <<additional_flags>>

Three files are required for SAMPEI to run:

Query/Target mgf files

A pair of mgf files is needed as input files with full path. One is used as query mgf file to perform conventional database search and provide high confidence query spectra. The other mgf file could be the same or different mgf file in which user want to uncover peptide with novel modifications not discovered by conventional search. Please make sure mgf file formated as one of the following examples.

Example 1:
BEGIN IONS
TITLE=Filename.390.390.3
RTINSECONDS=303.016
PEPMASS=442.230102539063 171650277.125
CHARGE=3+
129.1024323 379843.65625
130.0500488 108622.1875
136.0758667 226632.171875
148.0606232 279413.0625
173.0922699 26675.123046875
END IONS

Example 2:
BEGIN IONS
TITLE=Scan 4, Time=1.181370, MS2, HCD
PEPMASS=414.713379
CHARGE=2
120.438423 276.109863
121.133255 185.422791
122.366203 176.366150
127.615936 226.262482
127.961296 208.581024
127.989967 221.123886
END IONS

ID file

A separate tab-delimited (tsv) file produced by X!tandem or other database search tools needs to be provided. SAMPEI is applicable to different database search tools, as long as id file contains the following columns with designated column names as listed below.

Column name	Description	Example
scan	Scan id of the query scan (integer value)	1234
peptide	Peptide sequence identified by database search (string)	LPRSPPLKVLAE
modifications	Modification assigned to the sequence by database search (need to end with comma, and if multiple, separated by comma)	42.01057@A1,57.02147@C4,
charge	Charge state of the query scan	3
proteins	Protein names or accession number	sp_Q03052_PO3F1_HUMAN
Filename	Query mgf file name with no extension	KRG_MV411_G
expect	If using X!tandem in database search, otherwise optional	1.2e-08
total_MS2_intensity	If provided by X!tandem, otherwise optional	1659586.90743756

Example input files

Demo mgf and id files meet the package requirements can be download here.

Addiotional Flags

There are additional flags which can be set to fine tune the search parameters:

Flag	Default	Description
--error-type	ppm
--fragment-mass-error	20
--largest-gap-percent	0.4
--matched-peptide-intensity	0.5	The ratio of MS2 intensity of target scan matched to the theoretical fragments of peptide sequence over the summation of total MS2 intensity in the target scan
--matched-query-intensity	0.3	The ratio of MS2 intensity of query scan matched to target scan over the summation of total MS2 intensity in the query scan
--max-peaks-per-scan	20
--min-diff-dalton-bin	10	The absolute minimum dalton difference between the query scan and the target scan
--no-filter	False	Do not remove DB identified scans in the target mgf file
--output-directory	output	The directory where output files will be created
--write-intermediate	False	If specified both the unfiltered and filtered results will be written to file
--xtandem-xml		An X!tandem xml file which will be used for filtering results

Output

Output File

The output produced by SAMPEI has columns listed below.

Column name	Description	Example
MGF_query_file	Query mgf file name	190509_DL_OCIAML2_ACL_1.mgf
MGF_target_file	Target mgf file name	190509_DL_OCIAML2_ACL_1.mgf
Diff_dalton	Mass difference between query and target scan	71
Diff_dalton_bin	Integer mass difference between query and target scan	71.0378 71
Query_scan	Scan number of query spectra	49620
Query_scan_mz	Query scan m/z	759.7163086
Query_scan_charge	Query scan charge	3
Target_scan	Scan number of target spectra	33549
Target_scan_mz	Target scan m/z	783.3955688
Target_scan_charge	Target scan charge	3
Matches	Normalized number of matches	0.55
Matched_query	The percentage of MS2 intensity of query scan matched to target scan over the summation of total MS2 intensity in the query scan	0.611027774
Matched_intensity_product	percent matched query intensity times percent matched target intensity	0.237107605
Sum_log_intensity	Sum of log transformed query and target MS2 intensities	11.7649257
Peptide	Peptide sequence of target scan	GPAIGIDLGTTYSCVGVFQHGK
Modifications	Query scan modification	57.02147@C14,
Expect (Optional)	E value by X!tandem	0.00066
Total_MS2_intensity (Optional)	Query scan total MS2 intensity	2398832.919
Proteins	Protein name or id	sp_P54652_HSP72_HUMAN
Matched_peptide_intensity_max	The percentage of MS2 intensity of target scan matched to the theoretical fragments of peptide sequence over the summation of total MS2 intensity in the target scan	0.823
Largest_gap	The largest consecutive b/y ion missing	5
Largest_gap_percent	Largest gap over the length of the peptide sequence	0.227272727
Full_mod	Target scan modification	57.02147@C14,71.0377807617@I6,
Unique_mod	Target scan modification identified uniquely by SAMPEI	71.0377807617@I6,

Citing SAMPEI

Cifani, Li, Luo, Grivainis, Intlekofer, Fenyö, Kentsis. Discovery of protein modifications using high resolution differential mass spectrometry proteomics.