74	ProteomeXchange datasets
211	experiments
14,925	MS runs
444,752,369	spectra searched
120,422,937	PSMs
372,811	distinct peptides
16,178	canonical core proteins

About

The Maize PeptideAtlas provides a compendium of results from uniformly reprocessed mass spectrometry proteomics datasets.

Publicly-available Zea mays datasets were downloaded from ProteomeXchange and reprocessed from the raw files using the Trans-Proteomic Pipeline suite of tools.

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Chromosome Summary

Chromosome	Entries	Canonical		Uncertain		Redundant		Not Observed
Mitochondrial	163	16	9.8%	9	5.5%	18	11.0%	120	73.6%
Plastidial	111	41	36.9%	14	12.6%	21	18.9%	35	31.5%
Scaffolds	721	10	1.4%	22	3.1%	294	40.8%	395	54.8%
1	5,892	2,541	43.1%	598	10.1%	813	13.8%	1,940	32.9%
2	4,751	1,936	40.7%	491	10.3%	741	15.6%	1,583	33.3%
3	4,103	1,779	43.4%	448	10.9%	556	13.6%	1,320	32.2%
4	4,093	1,645	40.2%	390	9.5%	651	15.9%	1,407	34.4%
5	4,485	1,910	42.6%	470	10.5%	681	15.2%	1,424	31.8%
6	3,412	1,329	39.0%	381	11.2%	507	14.9%	1,195	35.0%
7	3,070	1,316	42.9%	296	9.6%	456	14.9%	1,002	32.6%
8	3,536	1,458	41.2%	359	10.2%	600	17.0%	1,119	31.6%
9	2,988	1,139	38.1%	328	11.0%	477	16.0%	1,044	34.9%
10	2,705	1,058	39.1%	263	9.7%	429	15.9%	955	35.3%
2023-09 Total	40,030	16,178	40.4%	4,069	10.2%	6,244	15.6%	13,539	33.8%

Column descriptions ▲

Entries: Number of entries in each chromosome
Canonical: Proteins seen with 2 distinct, uniquely mapping peptides
Uncertain: Proteins with some evidence that is not sufficient for canonical status
Redundant: Proteins that have peptides that map to them, but not uniquely and thus not needed to explain the observed peptides
Not Observed: No detections at all in PeptideAtlas above our very stringent threshold

Publications

A preprint describing this Maize PeptideAtlas 2023-09 build is available on bioRxiv: The Zea mays PeptideAtlas; a new maize community resource, Klaas J van Wijk, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, and Eric W Deutsch

Download

Below are individual Zea mays PeptideAtlas builds available for download in various flat file formats. Note that not all files contain all information from the build. A build subtitled "PSM FDR=0.002" denotes a PSM FDR threshold of 0.002 (0.2%) is applied to every sample in the build.

Maize 2023-09 PSM FDR = 0.00008Latest Build

Database tables exported as TSV dump file [348MB]
Database tables exported as mysql dump file [325MB]
Peptide CDS and chromosomal coordinates [752MB]
Peptide CDS coordinates [471MB]
Peptide sequences in FASTA format [10MB]

Help

Complete description of each of the available download formats

Maize Protein Sequences Download

Filename	Size	# Sequences	Description
V5_Zea_Mays_B73_core_proteome.fa	15M	40,030	Core proteome consists of one isoform per gene from the MaizeGDB proteome annotation from the Zea mays B73 version 5 genome assembly plus the mitochondrial and plastid proteomes from Refseq
Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.2.fa	30M	72,539	MaizeGDB proteome annotation from the Zea mays B73 version 5 genome assembly (multiple isoforms per gene) [ link ]
Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.protein.2.fa	93M	143,679	MaizeGDB proteome annotation from the Zea mays B73 version 4 genome assembly [ link ]
Zea_mays.AGPv3.22.pep.all.rename.2.fa	29M	63,241	MaizeGDB proteome annotation from the Zea mays B73 version 3 genome assembly [ link ]
Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.2.fa	25M	51,716	MaizeGDB proteome annotation from the Zea mays W22 cultivar genome assembly [ link ]
uniprot_2023.06.12_uID.remove.2.fa	31M	63,236	UniProtKB Zea mays reference proteome downloaded 2023-06-12 [ link ]
GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_protein.2.faa	29M	57,578	NCBI RefSeq proteome annotation from the Zea mays B73 version 5 genome assembly and Annotation Release 103 [ link ]
GCA_000005005.6_B73_RefGen_v4_protein.2.faa	69M	131,270	NCBI RefSeq proteome annotation from the Zea mays B73 version 4 genome assembly [ link ]
mitochondrion.2.fasta	48K	163	Zea mays mitochondrial proteome from NCBI RefSeq Zea mays B73 version 5
plastid.2.fasta	32K	111	Zea mays plastidial proteome from NCBI RefSeq Zea mays B73 version 5
contaminants.fasta	256K	499	PeptideAtlas custom set of 499 common contaminant proteins
crap_GFP.fasta	4.0K	3	Additional 3 fluorescent proteins eGFP, eYFP, RFP
Maize_PeptideAtlas_search.fasta	218M	456,684	Full database used in the searches

Other Resources

MaizeGDB: Maize Genetics and Genomics Database
PPDB: The Plant Proteome Database

Acknowledgements

We gratefully acknowledge the support for the Maize PeptideAtlas from NSF grant 1922871 “TRTech-PGR: A PeptideAtlas for Arabidopsis thaliana and other plant species; harnessing world-wide proteomics data and mining for biological features”.