<?php
//Вспомогательные функции предварительной инициализации
function SetupStore($location, $name, $mode)
{
    $store = new CPStore();
    $store->Open($location, $name, $mode);
    return $store;
}

function SetupCertificates($location, $name, $mode)
{
    $store = SetupStore($location, $name, $mode);
    $certs = $store->get_Certificates();
    return $certs;

}

function SetupCertificate($location, $name, $mode,
                           $find_type, $query, $valid_only,
                           $number)
{
    $certs = SetupCertificates($location, $name, $mode);
    if($find_type != NULL)
    {
        $certs = $certs->Find($find_type, $query, $valid_only);
        return $certs->Item($number);
    }
    else
    {
        $cert = $certs->Item($number);
        return $cert;
    }
}

function test_CPSignedData_Sign_Verify()
{
    try{
        $content = "test content";
        $address = "http://testca.cryptopro.ru/tsp/tsp.srf";
        $cert = SetupCertificate(CURRENT_USER_STORE, "My", STORE_OPEN_READ_ONLY,
                                 CERTIFICATE_FIND_SUBJECT_NAME, "Test", 0,
                                 1);

        if(!$cert)
            return "Certificate not found";
        $signer = new CPSigner();
        $signer->set_TSAAddress($address);
        $signer->set_Certificate($cert);

        $sd = new CPSignedData();
        $sd->set_ContentEncoding(1);
        $sd->set_Content(base64_encode($content));

        $sm = $sd->SignCades($signer, 1, false, 0);
        printf("Signature is:\n");
        printf($sm);
        printf("\n");
        $sd->Verify($sm, 0, VERIFY_SIGNATURE_ONLY);
        return 1;
    }catch(Exception $e)
    {
        printf($e->getMessage());
    }
}

if(test_CPSignedData_Sign_Verify() == 1)
{
    printf("TEST OK\n");
}else
{
    printf("TEST FAIL\n");
}

?>

public class CrypterService
{
    public byte[] MakeSign(byte[] data, string thumbprint, string pin)
    {
        string signature = "";
        string tspServerAddress = @"http://qs.cryptopro.ru/tsp/tsp.srf";

        CAdESCOM.CPStore pStore = new CAdESCOM.CPStore();
        pStore.Open(CAPICOM.CAPICOM_STORE_LOCATION.CAPICOM_LOCAL_MACHINE_STORE, "MY", CAPICOM.CAPICOM_STORE_OPEN_MODE.CAPICOM_STORE_OPEN_READ_ONLY | CAPICOM.CAPICOM_STORE_OPEN_MODE.CAPICOM_STORE_OPEN_EXISTING_ONLY);
        CAPICOM.ICertificates certificatesFromStore = pStore.Certificates;
        CAPICOM.Certificate certificate = GetCertificates(certificatesFromStore).Find(x=> x.Thumbprint.ToLower() == thumbprint.ToLower());

        CPSigner cpsigner = new CPSigner
        {
            Certificate = certificate,
            //KeyPin = pin,
            KeyPin = Encoding.ASCII.GetString(Encoding.Unicode.GetBytes(pin)),
            TSAAddress = tspServerAddress,
            Options = CAPICOM_CERTIFICATE_INCLUDE_OPTION.CAPICOM_CERTIFICATE_INCLUDE_WHOLE_CHAIN
        };
        CadesSignedData cadesSignedData = new CadesSignedData
        {
            ContentEncoding = CADESCOM_CONTENT_ENCODING_TYPE.CADESCOM_BASE64_TO_BINARY,
            Content = Convert.ToBase64String(data)
        };

        signature = cadesSignedData.SignCades(cpsigner, CADESCOM_CADES_TYPE.CADESCOM_CADES_BES, true, CAdESCOM.CAPICOM_ENCODING_TYPE.CAPICOM_ENCODE_BASE64);
        cadesSignedData.VerifyCades(signature, CADESCOM_CADES_TYPE.CADESCOM_CADES_BES, true);

        return Convert.FromBase64String(signature);
    }

    private List<CAPICOM.Certificate> GetCertificates(ICertificates certificates)
    {
        List<CAPICOM.Certificate> certs = new List<Certificate>();
        for (int i = 0; i < certificates.Count; i++)
        {
            try
            {
                certs.Add((CAPICOM.Certificate)certificates[i]);
            }
            catch { }
        }
        return certs;
    }
}